Biomarkers for autism spectrum disorders

ABSTRACT

Methods of determining the risk of ASD in an individual are provided which comprise identifying the presence of one or more genomic mutations in one or more of the genes, PTCHD1, SHANK3, NFIA, DPP6, DPP10, DYPD, GPR98, PQBP1, ZNF41 and FTSJ1.

FIELD OF THE INVENTION

The present invention relates to genetic markers for Autism Spectrum Disorders (ASD).

BACKGROUND OF THE INVENTION

Autism is a heritable neurodevelopmental condition characterized by impairments in social communication and by a preference for repetitive activities. Autism is not a distinct categorical disorder but is the prototype of a group of conditions defined as Pervasive Developmental Disorders (PDDs) or Autism Spectrum Disorders (ASD), which include Asperger's Disorder, Childhood Disintegrative Disorder, Pervasive developmental disorder—not otherwise specified (PDD-NOS) and Rett Syndrome. ASD is diagnosed in families of all racial, ethnic and social-economic backgrounds with incidence roughly four times higher in males compared to females. Overall population prevalence of autism has increased in recent years to a current estimate of 20 in 10,000 with incidence as high as 60 in 10,000 for all autism spectrum disorders.

Data from several epidemiological twin and family studies provide substantial evidence that autism has a significant and complex genetic etiology. The concordance rate in monozygotic twins is 60-90% (Bailey 1995), and the recurrence rate in siblings of affected probands has been reported to be between 5-10% (Jones & Szatmari 1988) representing a 50 fold increase in risk compared to the general population. Although autism spectrum disorders are among the most heritable complex disorders, the genetic risk is clearly not conferred in simple Mendelian fashion.

In a minority of cases (˜10%), autism is part of a broader recognizable disorder (e.g. fragile X syndrome, tuberous sclerosis) or is associated with cytogenetically-detectable chromosome abnormalities. Moreover, co-morbidity of autism with microdeletion syndromes (e.g. William-Beuren and Sotos) and other genomic disorders (e.g. Prader-Willi/Angelman) suggests chromosomal imbalances are involved in the underlying etiology. The most frequent cytogenetic anomaly is an interstitial, maternally-inherited duplication of 15q11-13 (1-3%) encompassing the Prader Willi/Angelman Syndrome critical region. There are also a large number of cases with deletions in the q11.2 and q13.3 regions of chromosome 22. The 22q11.2 region is associated with velo-cardio-facial Syndrome and deletions at 22q13.3 appear to also represent a clinically definable syndrome. Both deletions are associated with the autistic phenotypes. Other chromosome loci associated with anomalies with a higher frequency of events observed in syndromic forms of ASD include 7q (see TCAG www.chr7.org), 2q37, 5p14-15, 17p112. In addition, reciprocal duplications overlapping the William-Beuren deletion region have been associated with the autism phenotype.

Genome-wide linkage scans have found evidence for susceptibility loci on almost all chromosomes with 7q yielding the most consistent results. Other loci with significant linkage include 2q (IMGSAC 2001), 3q and most recently 11p (AGP 10K study). In some instances, like 7q, there is considerable overlap between cytogenetic anomalies and linkage results. However, the lack of linkage found at 15q11-13 and 22q13.3 loci reflect considerable heterogeneity in ASD and suggest that these rearrangements are responsible for a particular ASD subtype involving genes that do not contribute to the phenotype in cytogenetically normal patients. Despite promising results, no specific genes within these linkage peaks have unequivocally been shown to contribute to autism.

Mutations associated with ASD have been reported in two neuroligin (NLGN3 and NLGN4) genes and more recently SHANK3; however, these account for only rare causes of ASD. Other genes have been implicated, but represent rare events or have not yet been validated by other studies.

Together these data suggest substantial genetic heterogeneity with the most likely cause of non-syndromic idiopathic ASD involving multiple epistatically-interacting loci.

The identification of large scale copy number variants (CNVs) represents a considerable source of genetic variation in the human genome that contributes to phenotypic variation and disease susceptibility found small inherited deletions in autistic kindreds suggesting possible susceptibility loci.

It would be desirable to identify genetic markers of ASD that facilitate in a determination of the risk of ASD in an individual, as well as to assist in the diagnosis of the condition.

SUMMARY OF THE INVENTION

A number of genetic markers have now been identified which are useful in assessing the risk of ASD in an individual, as well as being useful to diagnose the condition. The markers are useful both individually and in the form of a microarray to screen individuals for risk of ASD.

Thus, in one aspect of the present invention, a method of determining the risk of ASD in an individual is provided comprising:

probing a nucleic acid-containing sample obtained from the individual for a gene encoding PTCHD1, wherein a determination that the gene comprises a deletion of at least a portion of exon 1 is indicative of a risk of ASD in the individual.

In another aspect of the present invention, a method of determining the risk of ASD in an individual is provided comprising:

probing a nucleic acid-containing sample obtained from the individual for a mutation that modulates the expression of at least one gene selected from the group consisting of PTCHD1, SHANK3, NFIA, DPP6, DPP10, GPR98, PQBP1, ZNF41 and FTSJ1, wherein identification of a mutation that modulates the expression of at least one of said genes is indicative of a risk of ASD.

In another aspect of the invention, a method of determining the risk of ASD in an individual is provided comprising:

screening a biological sample obtained from the individual for abnormal levels of at least one gene product expressed by a gene selected from the group consisting of PTCHD1, SHANK3, NFIA, DPP6, DPP10, GPR98, PQBP1, ZNF41 and FTSJ1, wherein a determination that at least one of said gene products is expressed at a level that varies from the level in a healthy non-ASD individual is indicative of a risk of ASD.

In a further aspect of the invention, a method of determining the risk of ASD in an individual is provided comprising:

screening a nucleic acid-containing sample from the individual for genomic sequence variations that modulate the expression of PTCHD1.

These and other aspects of the present invention are described by reference to the following figures in which:

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 is a flow chart depicting the methodology used to identify ASD-specific CNVs;

FIG. 2 illustrates a genome-wide distribution of ASD-specific CNVs as described in Table 3;

FIG. 3 illustrates the chromosome 16p11.2 region as depicted in the Autism Chromosome Rearrangement Database;

FIG. 4 illustrates examples of CNVs observed in ASD families including probands having multiple de novo events (a); rearrangements in the SHANK3 gene (b); probands with chromosome X deletions (at PTCHD1) from female carriers (c) or inherited translocations in addition to an unrelated de novo deletion (d); overlapping events in unrelated probands either de novo (e) or inherited (t) at the DPP6 locus; and recurrent de novo events at chromosome 16p11.2 in unrelated probands either gains (h) or losses (g);

FIG. 5 illustrates examples of DPP6 and DPP10 ASD-related CNVs;

FIG. 6 illustrates examples of chromosome 22q11.2 and 16p11.2 ASD-related CNVs;

FIG. 7 illustrates the cDNA sequence (A) of the PTCHD1 gene and the corresponding amino acid sequence (B); and

FIG. 8 illustrates ASD-related missense mutations identified in Table 7.

DETAILED DESCRIPTION OF THE INVENTION

A method of determining the risk of an autism spectrum disorder (ASD) in an individual is provided comprising screening a biological sample obtained from the individual for a mutation that may modulate the expression of at least one gene selected from the group consisting of PTCHD1, SHANK3, NFIA, DPP6, DPP10, DPYD, GPR98, PQBP1, ZNF41 and FTSJ1. Such genes are referred to herein as “ASD-associated” genes.

The term “an autism spectrum disorder” or “an ASD” is used herein to refer to at least one condition that results in developmental delay of an individual such as autism, Asperger's Disorder, Childhood Disintegrative Disorder, Pervasive Developmental Disorder—Not Otherwise Specified (PDD-NOS) and Rett Syndrome (APA DSM-IV 2000).

In the present method of determining ASD risk in an individual, a biological sample obtained from the individual is utilized. A suitable biological sample may include, for example, a nucleic acid-containing sample or a protein-containing sample. Examples of suitable biological samples include saliva, urine, semen, other bodily fluids or secretions, epithelial cells, cheek cells, hair and the like. Although such non-invasively obtained biological samples are preferred for use in the present method, one of skill in the art will appreciate that invasively-obtained biological samples, may also be used in the method, including for example, blood, serum, bone marrow, cerebrospinal fluid (CSF) and tissue biopsies such as tissue from the cerebellum, spinal cord, prostate, stomach, uterus, small intestine and mammary gland samples. Techniques for the invasive process of obtaining such samples are known to those of skill in the art. The present method may also be utilized in prenatal testing for the risk of ASD using an appropriate biological sample such as amniotic fluid and chorionic villus.

In one aspect, the biological sample is screened for nucleic acid encoding selected genes in order to detect mutations associated with an ASD. It may be necessary, or preferable, to extract the nucleic acid from the biological sample prior to screening the sample. Methods of nucleic acid extraction are well-known to those of skill in the art and include chemical extraction techniques utilizing phenol-chloroform (Sambrook et al., 1989), guanidine-containing solutions, or CTAB-containing buffers. As well, as a matter of convenience, commercial DNA extraction kits are also widely available from laboratory reagent supply companies, including for example, the QIAamp DNA Blood Minikit available from QIAGEN (Chatsworth, Calif.), or the Extract-N-Amp blood kit available from Sigma (St. Louis, Mo.).

Once an appropriate nucleic acid sample is obtained, it is subjected to well-established methods of screening, such as those described in the specific examples that follow, to detect genetic mutations indicative of ASD, i.e. ASD-linked mutations. Mutations, such as genomic copy number variations (CNVs), which include gains and deletions of segments of DNA, for example, segments of DNA greater than about 1 kb, such as DNA segments between about 300 and 500 kb, as well as base pair mutations such as nonsense, missense and splice site mutations, including sequence mutations in both coding and regulatory regions of a gene, have been found to be indicative of ASD.

ASD-linked mutations such as CNVs are not restricted to a single chromosome, but rather have been detected on a multiple chromosomes such as the X chromosome, chromosome 15 and chromosome 21, and on various regions of the same chromosome such as at Xp11 and Xp22. Examples of CNVs that have been determined to be linked to ASD include a deletion on chromosome Xp22 including at least a portion of exon 1 of the PTCHD1 gene; a duplication on chromosome 15q11; and a deletion within the SHANK3 gene.

Genomic sequence variations of various types in different genes have been identified as indicative of ASD. CNVs in the DPP10 gene, including intronic gains, such as a 105 kb intronic gain, and exonic losses, such as a 478 kb exonic loss, both of which are more specifically identified in Table 1, have been identified; CNVs in the DPP6 gene, such as a 66 kb loss encompassing exons 2 and 3 and gains such as a CNV encompassing the entire DPP6 gene, a 270 kb exonic gain (exon 1), and a 16 kb intronic gain (see Table 1); CNVs in the SHANK3 gene such as a 276 kb loss; and CNVs in the DYPD gene such as a loss of the entire gene.

In one embodiment, genomic sequence variations that inhibit the expression of PTCHD1 have been linked to ASD. The terminology “inhibit expression” refers broadly to sequence variations that may inhibit, or at least reduce, any one of transcription and/or translation, as well as the activity of the PTCHD1 protein. For example, a CNV in the PTCHD1 gene comprising a large deletion of the coding region which results in at least a reduction of the expression of PTCHD1 protein has been found to be indicative of ASD. Although the CNV is not particularly restricted, the CNV deletion may include, for example, at least a portion of exon 1, but may additionally include surrounding regions as well, such as intron 1, in whole or in part, or a portion or more of the upstream region thereof.

Genomic sequence variations other than CNVs have also been found to be indicative of ASD, including, for example, missense mutations which result in amino acid changes in a protein that may also affect protein expression. In one embodiment, missense mutations in the PTCHD1 gene have been identified which are indicative of ASD, including missense mutations resulting in the following amino acid substitutions in the Ptchd1 protein: L73F, I173V, V195I, ML336-337II and E479G.

To determine risk of ASD in an individual, it may be advantageous to screen for multiple genomic mutations, including CNVs and other mutations as indicated above applying array technology. In this regard, genomic sequencing and profiling, using well-established techniques as exemplified herein in the specific examples, may be conducted for an individual to be assessed with respect to ASD risk/diagnosis using a suitable biological sample obtained from the individual. Identification of one or more mutations associated with ASD would be indicative of a risk of ASD, or may be indicative of a diagnosis of ASD. This analysis may be conducted in combination with an evaluation of other characteristics of the individual being assessed, including for example, phenotypic characteristics.

In view of the determination of gene mutations which are linked to ASD, a method for determining risk of ASD in an individual is also provided in which the expression or activity of a product of an ASD-linked gene mutation is determined in a biological protein-containing sample obtained from the individual. Abnormal levels of the gene product or abnormal levels of the activity thereof, i.e. reduced or elevated levels, in comparison with levels that exist in healthy non-ASD individuals, are indicative of a risk of ASD, or may be indicative of ASD. Thus, a determination of the level and/or activity of the gene products of one or more of PTCHD1, SHANK3, NFIA, DPP6, DPP10, DYPD, GPR98, PQBP1, ZNF41 and FTSJ1, may be used to determine the risk of ASD in an individual, or to diagnose ASD. As one of skill in the art will appreciate, standard assays may be used to identify and quantify the presence and/or activity of a selected gene product.

Embodiments of the invention are described by reference to the following specific examples which is not to be construed as limiting.

Example 1 DNA Samples and Population Structure

The study included 426 ASD families. All of the index cases met Autism Diagnostic Interview-Revised (ADI-R) and Autism Diagnostic Observation Schedule (ADOS) criteria or on a clinical best estimate (Risi et al. J Am Acad Child Adolesc Psychiatry 2006; 45(9):1094-103). Thirty-two of these carried a cytogenetic chromosome rearrangement; 18 were detected by karyotyping 328 of 412 samples that originated from child diagnostic centres at the Hospital for Sick Children in Toronto and from St. John's, Newfoundland; 14 were already known to carry karyotypic anomalies (see Table 1 for information on these 32 patients). Affected and unaffected siblings were also assessed, and 56% (237/426) had one child (simplex) and 44% (189/426) had more than one child (multiplex) with ASD. Most cases were screened for fragile X mutations (75%) and if detected they were not included in the study. Most experiments were performed on blood genomic DNA (80%), otherwise the source was cell lines, e.g. lymphoblast cell lines. Population ancestry was estimated using STRUCTURE (Falush et al. Genetics 2003; 164(4):1567-87; Pritchard et al. Genetics 2000; 155(2):945-59).

TABLE 1 Cytogenetic Analysis Sample Phenotype/Family Breakpoint CNV Analysis ID type Karyotype Location RefSeq Genes Chr CNV Size (bp) Location AS/Str^(a) RefSeq Genes Comments 1 NA0008- Simplex family 46, XX, 2q33.1: SATB2 2p11.2 Loss 917,200 89,056,400- No/NS No known genes NFLD 000 ASD, developmental t(2; 6)(q32; p22) 200,096,682- 89,973,600 (50863L) dyspraxia unknown 200,154,790 6p22.3: No known genes 6p21.33 Gain  54,600 30,134,300- Yes/NS ZNRD1, 21,561,566- 30,188,900 PPP1R11, 21,644,040 RNF39, TRIM31 11p13 Gain  54,200 35,332,700- No/NS SLC1A2 35,386,900 13q21.33 Loss  28,200 69,642,500- No/NS No known genes 69,670,700 14q11.2 Gain 549,300 21,490,300- No/NS No known genes 22,039,600 14q32.33 Loss  64,000 106,152,000- No/NS No known genes 106,216,000 2 NA0005- Simplex family 46, XX, 4q21.3 Several 1p13.2 Gain 128,963 112,783,876- Yes/NS ST7L, CAPZA1 NFLD 000 ASD, seizure t(4; 5)(q21; q13) 112,912,839 (53601L) disorder, obesity, unknown 2q37.3 Loss 602,914 242,127,468- No/S 10 genes macrocephaly Error! 242,730,382 Hyperlink reference not valid. 3q29 Loss  43,033 196,922,636- No/NS MUC20, MUC4 196,965,669 5q14.2-q14.3: Several 5q15 Loss  48,627 97,076,449- No/NS No known genes 82,802,678- 97,125,076 91,285,973 5q21.3 Loss  13,000 109,391,000- Yes/NS No known genes 109,404,000 8p23.1 Gain 448,146 12,039,387- No/S FAM86B1, 12,487,533 DEFB130, LOC440053 14q11.2 Gain 223,579 19,272,965- No/S 6 OR genes 19,496,544 14q11.2 Gain 650,430 21,407,981- No/S No known genes 22,058,411 15q11.2 Gain 1,642,961  18,446,422- No/NS LOC283755, Error! 20,089,383 POTE15, Hyperlink OR4M2, OR4N4 reference not valid. 3 NA0039- Simplex family 46, XX, See CNV See CNV 9q32 Gain 498,000 114,038,000- No/NS 7 genes NFLD 000 ASD, submucous der(22)t(14; 22) 114,536,000 Unaffected sibling (69736) cleft, globally (q32; q13) pat 14q32.33 Gain 1,436,000  104,920,000- No/NS 6 genes with ADHD has developmentally inherited 106,356,000 46, XX, der(14) delayed, large ears, 15q13.3 Gain 502,500 29,796,300- No/NS CHRNA7 t(14; 22)(q32; q13) short forehead, 30,298,800 distally tapere 22q13.31- Loss 3,231,700  46,277,400- Yes/NS 40 genes + fingers, severe pes q31.33 49,509,100 SHANK3 planovalgus 4 SK0283- Simplex family 47, XX, See CNV See CNV 1p22.3 Gain  23,993 87,417,351- Yes/NS No known genes SK 003 ASD ring chromosome 1 87,441,344 (72309) de novo 1q21.2- Gain 1,451,926  148,095,537- Yes/S 36 genes q21.3 149,547,463 3p26.1 Loss  44,458 5,365,506- Yes/S No known genes 5,409,964 4p13 Gain  95,508 44,762,996- Yes/S No known genes 44,858,504 4q33 Loss  82,224 171,715,627- Yes/NS No known genes 171,797,851 5q31.3 Loss 355,649 140,658,658- Yes/NS 6 genes 141,014,307 6p12.3 Gain  13,950 46,962,122- No/NS GPR116 46,976,072 7p14.1 Loss 102,939 38,041,635- No/NS STARD3NL, 38,144,574 TARP 7q34 Loss 169,191 141,813,948- No/NS PRSS1 141,983,139 14q11.2 Loss 583,148 21,455,546- No/S No known genes 22,038,694 15q11.2 Loss 1,632,769  18,427,103- No/S LOC283755, 20,059,872 POTE15, OR4M2, OR4N4 17q21.31 Loss 140,746 41,570,665- No/NS KIAA1267 41,711,411 5 SK0044- Simplex family 46, XY, 1p31.1: NEGR1 7p14.1 Gain  85,900 39,828,000- No/NS CDC2L5 SK 003 ASD t(1; 2)(p22.1; 72,065,578- 39,913,900 (50067) p23)pat der(13; 72,163,007 15)(q10; q10)mat 2p24.3: No known genes inherited 12,376,807- 12,733,637 13q10: in progress 15q10: in progress 6 SK0182- Simplex family 46 XY, 1q24.2: No known genes 2p24.3 Gain  15,100 14,304,500- No/NS No known genes SK 003 ASD t(1; 9)(q25; p13) 167,452,268- 14,319,600 Younger brother (52065) inherited 167,522,136 has the same 9p12: No known genes 14q11.2 Gain 288,100 19,204,300- No/S 6 genes translocation and 45,695,701- 19,492,400 severe speech 45,737,008 and language disorder but does not meet ASD criteria on ADOS. 7 SK0335- Simplex Family 46, XX, 2q23.1: LOC401431, 2p13.3 Gain 374,900 70,152,900- Yes/NS 6 genes Others 003 ASD, mental t(2; 10)(q22; 148,938,284- ATP6VOE2 70,527,800 Non-Canadian (72815) retardation q22.3) 149,125,547 family unknown 10q23.31: SLC16A12, 3q29 Gain  43,033 196,922,636- No/NS MUC20, MUC4 91,265,490- PANK1, 196,965,669 91,461,660 MPHOSPH1 5p13.1 Loss 272,618 38,534,384- Yes/S LIFR 38,807,002 6p21.32 Gain 162,900 32,344,099- Yes/NS C6orf10, BTNL2 32,506,999 8p23.1 Gain  21,783 12,264,620- No/NS No known genes 12,286,403 9q32 Gain  22,000 114,153,000- No/S ORM1, ORM2 114,175,000 14q11.2 Gain 331,503 21,717,112- No/S No known genes 22,048,615 15q11.2 Gain 1,516,085  18,427,100- No/S LOC283755, 19,943,185 POTE15, OR4M2, OR4N4 16p11.2- Gain 266,336 34,325,041- No/NS No known genes 11.1 34,591,377 17q21.31 Gain 201,731 41,518,102- No/S KIAA1267 41,719,833 20p12.1 Loss  27,500 14,973,800- Yes/S C20orf133 15,001,300 8 SK0126- Multiplex family 46, XY, 2p11.2: No known genes 2q34 Loss  3,000 213,013,000- Yes/NS ERBB4 Other 003 ASD t(2; 11)(p11.2; 89,117,655- 213,016,000 Canadian Family (59144) q13.3) pat 89,158,494 inherited 11q13.1: POLA2, 64,821,333- CDC42EP2, 64,861,285 DPF2 9 SK0152- Multiplex family 46, XY, 3p24: not 3p25.1- Loss 1,409,600  15,125,800- Yes/S 12 genes Other 003 ASD, oral motor inv(3)(p24; q24), available p24.3 16,535,400 Canadian Family (41548L) apraxia, poor balance t(5; 7)(p15p13) 3q24: not 3p12.3 Gain  55,000 78,902,000- Yes/S ROBO1 Previously and coordination, de novo available 78,957,000 described in a mild hypotonia, walks 5p14.3: CDH18 5p15.31- Loss 3,429,389  9,275,811- Yes/S 8 genes manuscript by with a wide gait, 19,825,926- p15.2 12,705,200 Harvard et al¹. severe language 19,883,410 The 3p25.1, delay, moderate 7p13: No known genes 6q16.1 Loss  60,058 95,556,287- No/S No known genes 5p15.31-p15.2 intellectual disability, 46,618,434- 95,616,345 and 18q12.2 some facial features 46,733,542 7p14.1 Gain  35,243 38,096,725- No/NS No known genes deletions were of Cri du Chat 38,131,968 identified in 10q11.22 Gain 455,130 47,030,119- No/S ANXA8 Harvard, C. et al 47,485,249 using BAC CGH. 12p11.21 Gain  63,728 31,904,362- No/S No known genes The deletion size 31,968,090 has been refined 12q12 Loss 422,842 40,584,198- Yes/S YAF2, ZCRB1 here using SNPs. 41,007,040 Older sibling also 14q11.2 Gain 491,397 21,584,229- No/S No known genes has ASD but has 22,075,626 a normal 46, XX 14q32.33 Gain  22,269 106,223,861- No/NS No known genes karyotype 106,246,130 Maternal aunt with 15q11.2 Loss 1,632,718  18,446,422- No/S LOC283755, schizophrenia and 20,079,140 POTE15, a maternal uncle OR4M2, OR4N4 with Down 16q21 Loss  91,432 63,768,909- Yes/NS No known genes syndrome 63,860,341 17q21.31 Gain 219,797 41,500,036- No/NS KIAA1267 41,719,833 18q12.2 Loss 816,914 32,174,061- Yes/S KIAA1328, 32,990,975 C18orf10, FHOD3 10 SK0105- Multiplex family 46, XY, 4p15.3: No known genes 10q11.21 Gain 1,098,400  41,956,500- Yes/NS RET, SK 003 ASD, primarily non- inv(4)(p12; 12,173,445- 43,054,900 RASGEF1A, Described (27155L) verbal, profound p15.3)mat 12,335,572 BMS1L, ZNF11B, previously in developmental delay inherited MGC16291, Vincent et al.² GALNACT-2 Affected brother, 4p12: GABRG1 13q14.2 Gain 162,300 47,414,800- Yes/NS MED4, NUDT15, apparently 44,876,353- (breakpoint region 47,577,100 SUCLA2 unaffected mother 46,024,486 is located in 16q21 Loss  56,600 61,854,900- Yes/NS No known genes and unaffected intron 7) 61,911,500 maternal 17q21.31 Gain 238,600 41,521,600- No/NS KIAA1267 grandfather all 41,760,200 have the same inversion. Distal 4p15.3 breakpoint maps ~12 Mb to a region previously indicated to show linkage to autism. 11 SK0205- Simplex family 46, XX, See CNV See CNV 3q29 Gain  96,068 199,226,000- No/NS LMLN, SK 004 ASD del(5)(p15.1) 199,322,068 LOC348840 FISH analysis with (56242) de novo 5p15.33- Loss 13,800,984   81,949- Yes/S >50 genes subtelomeric p15.2 13,882,933 probe (containing 5q15 Loss  70,891 97,054,185- No/NS No known genes D5S2488) was 97,125,076 consistent with a 10q11.22 Gain 1,121,866  46,363,383- No/S SYT15, ANXA8, terminal deletion 47,485,249 ANXA8L1, on 5p. PPYR1, GPRIN2 10q21.3 Loss  29,732 67,747,770- No/NS CTNNA3 67,777,502 10q26.3 Gain 244,432 135,079,000- No/S SYCE1; CYP2E1 135,323,432 14q11.2 Gain 217,035 19,272,965- No/S OR4K1, OR4N2, 19,490,000 OR4K5, OR4K2 15q11.2 Gain 1,662,300  18,427,100- No/S LOC283755, 20,089,400 POTE15, OR4M2, OR4N4 17q21.31 Gain  65,845 41,006,823- No/S No known genes 41,072,668 17q21.31 Gain 187,028 41,521,621- No/NS KIAA1267 41,708,649 22q11.21 Gain 150,753 17,265,500- No/S DGCR6, PRODH, 17,416,253 DGCR2 12 SK0061- Simplex family 46, XY, 7q31.31: No known genes No CNV detected Other 003 ASD, developmental t(5; 7)(q15; 118,928,065- Non-Canadian (44951) delay q31.32) 119,006,076 Family unknown 5q14.3: No known genes 88,849,193- 88,891,151 13 SK0195- Simplex family 46, XY, 5q31.1: KLHL3 2p16.1 Gain  47,900 57,314,000- No/NS No known genes Other 003 ASD t(5; 8; 17) 136,979,583- 57,361,900 Canadian Family (55310) (q31.1; q24.1; 137,038,092 q21.3) 8q24.22: No known genes 10q23.1 Loss  17,500 83,772,000- Yes/NS NRG de novo 132,448,049- 83,789,500 132,512,973 17q21.31: LRRC37A2, 14q11.2 Gain 288,100 19,204,300- No/NS OR4K1, OR4N2, 41,893,216- ARL17P1, 19,492,400 OR4M1, OR4K5, 42,093,636 LOC641522, NSF OR4Q3, OR4K2 17q21.31 Gain 644,700 41,521,600- No/S KIAA1267 42,166,300 14 SK0133- Simplex family 46, XY, 6p12.1: DST, c6orf65 2q37.1 Gain 314,000 232,076,000- Yes/NS MGC43122, Other 003 ASD t(6; 7)(p11.2; 56,805,919- 232,390,000 NMUR1, Canadian Family (46012) q22)pat 56,967,398 MGC35154, NCL, CNV seen at inherited B3GNT7 11q25 is in the 7q22.1: No known genes 5q14.3 Gain 633,400 89,492,800- Yes/NS CETN3, same breakpoint 97,933,646- 90,126,200 LOC153364, region as Sample 97,973,368 POLR3G, SK0145-003 MASS1 7q33 Loss  3,000 136,255,000- No/NS No known genes 136,258,000 8q23.2 Loss  32,000 111,182,000- No/NS No known genes 111,214,000 9p21.3 Loss  8,200 25,073,900- Yes/NS No known genes 25,082,100 11q25 Gain 369,000 133,855,000- No/S No known genes 134,224,000 12q21.33 Gain  19,700 90,807,700- Yes/NS No known genes 90,827,400 13q21.32 Loss  2,500 65,576,300- Yes/NS No known genes 65,578,800 15 SK0043- Multiplex family 46, XY, 6q11.2-q12: No known genes 8p23.2 Loss  35,040 3,984,190- No/NS CSMD1 SK 003 ASD t(6; 9)(q10; q12) 63,464,452- 4,019,230 Sibling also has (29346) unknown 63,511,410 ASD but a normal 9q21.11: PIP5K1B 15q11.2 Gain 1,713,200  18,376,200- No/S LOC283755, 46, XY karyotype 68,599,032- 20,089,400 POTE15, 68,682,365 OR4M2, OR4N4 16 SK0181- Simplex family 46, XY, 6q12: No known genes 3p14.1- Loss 5,346,900  65,286,300- Yes/S 13 genes SK 004 ASD t(6; 14)(q13; q21) 69,241,818- p13 70,633,200 (52191) de novo 69,279,457 14q21.1-q21.2: LRFN5, c14orf155, 4q28.3 Loss 254,000 135,282,000- No/NS No known genes 40,807,716- c14orf28, BTBD5, 135,536,000 44,806,460 KIAA0423, PRPF39, FKBP3, AK093422, KIAA1596, FANCM, c14orf106 17 SK0083- Simplex family 46, XY, 7q31.1: IMMP2L, LRRN3, 1q31.1 Loss  15,000 186,702,000- No/S No known genes Other 003 ASD, del(7)(q31.1q31.32) 108,272,363- DOCK4, ZNF277P, 186,717,000 Canadian Family (50800L) craniosynostosis, de novo 108,337,904 IFRD1 . . . to . . . Described developmental verbal 7q31.31: ASZ1, CFTR, 2p23.3 Gain  26,300 25,138,000- Yes/NS No known genes previously in Feuk dyspraxia, motor 119,007,999- CTTNBP2, LSM8, 25,164,300 et al.³ delay 119,335,246 ANKRD7 4q35.2 Gain  21,314 188,232,000- Yes/S No known genes 188,253,314 6p24.2 Gain 188,500 11,479,600- Yes/NS No known genes 11,668,100 7q31.1- Loss 11,023,506   108,200,381- Yes/S >50 genes q31.31 119,223,887 7q36.2 Loss  26,297 152,027,450- Yes/NS No known genes 152,053,747 8q24.21 Gain  48,000 127,951,000- Yes/NS No known genes 127,999,000 10p11.23 Gain  26,700 30,893,400- Yes/NS No known genes 30,920,100 14q11.2 Loss 219,458 19,272,965- No/S OR4K1, OR4N2, 19,492,423 OR4M1, OR4K5, OR4Q3, OR4K2 17q21.31 Loss 117,521 40,897,617- No/NS PLEKHM1 41,015,138 18 SK0131- Simplex family 46, XX, 7q31.1: FOXP2, MDFIC, 2p22.2 Gain  67,740 37,848,232- No/NS No known genes Other 003 Autistic features, del(7)(q31.2q32.2) 113,181,975- TFEC, TES, 37,915,972 Canadian Family (39989) speech-language (D7S486-, D7S522-) 113,518,235 CAV2, CAV1 . . . 3p21.31 Gain  52,599 147,754,068- Yes/NS CCR5, CCRL2, Described disorder de novo, to . . . IRF5, 147,806,667 CCR2 previously in Feuk (developmental WBS inv-2 7q32.2: TNPO3, TSPAN33, 4q31.21 Gain 120,171 145,146,000- No/S GYPE et al.³ verbal dyspraxia), de novo 128,540,690- SMO, FAM40B, 145,266,171 dysmorphic features, 128,796,716 KIAA0828 7p14.1 Gain 147,076 38,096,725- No/NS AMPH mild developmental 38,243,801 delay, unable to 7q31.1- Loss 15,486,721   113,335,000- Yes/S >50 genes cough/sneeze/laugh q32.2 128,821,721 spontaneously 8q13.3 Gain 261,985 72,881,221- Yes/NS MSC, TRPA1 73,143,206 10q11.22 Gain 455,100 47,030,100- No/NS ANXA8 47,485,200 10q26.2 Gain  91,077 128,501,014- Yes/S DOCK1 128,592,091 13q21.33 Loss  44,235 69,634,065- No/NS No known genes 69,678,300 14q11.2 Loss 222,786 19,272,965- No/NS OR4K1, OR4N2, 19,495,751 OR4M1, OR4K5, OR4Q3, OR4K2 14q11.2 Gain 637,249 21,462,466- No/S No known genes 22,099,715 15q11.2 Gain 1,662,280  18,427,103- No/NS LOC283755, 20,089,383 POTE15, OR4M2, OR4N4 17q12 Gain  29,984 31,471,515- No/NS No known genes 31,501,499 22q11.22 Gain 810,876 20,772,047- No/NS 6 genes 21,582,923 19 SK0002- Simplex family 46, XX, 7p21.1: No known genes 4q28.3 Gain 765,000 132,195,000- No/S No known genes Other 003 ASD, psychosis inv(7)(p15.3; 18,284,397- 132,960,000 Non Canadian- (50002) q22.1) 18,302,387 Family unknown 7q22.3: SPRK2 5p15.1- Gain 239,100 14,940,400- No/S No known genes 104,360,659- 15.2 15,179,500 104,549,945 15q11.2 Gain 1,713,200  18,376,200- Yes/S LOC283755, 20,089,400 POTE15, OR4M2, OR4N4 20 SK0211- Simplex family 46, XX, 7q21.3: No known genes 7q22.1 Gain 379,000 100,393,000- No/NS 10 genes Other 003 ASD, mild elevation inv(7)(q22q34)mat 96,943,657- 100,772,000 Non Canadian (58892) of lactate inherited 96,985,663 Family 7q34: TAS2R4, TAS2R5 9p21.1 Loss 135,100 30,408,400- No/NS No known genes Mother and 140,920,721- 30,543,500 unaffected twin 140,958,207 sister have the same karyotype; 7q34 breakpoint overlaps with a ASD translocation patient 21 SK0040- Multiplex family 46, XY, 7p15.3: No known genes 2q37.3 Loss  95,959 242,634,423- No/S No known genes Other 003 ASD, ADHD, severe t(7; 8)(p15; q22), 21,825,126- 242,730,382 Non-Canadian (55449) anxiety attacks, t (10; 11)(q26; 21,869,196 Family seizures, difficulties q23) 8q22.2: STK3 10q21.3 Loss 144,903 67,734,600- No/S CTNNA3 Unaffected sister with fine and gross unknown 99,652,299- 67,879,503 with normal motor skills 99,823,618 11q22.3 Loss  62,995 104,729,456- No/NS No know genes female karyotype, 104,792,451 has difficulties in 10q26: Multiple genes 14q11.2 Gain 219,458 19,272,965- No/NS OR4K2, OR4N2, some muscles, 127,985,179- 19,492,423 OR4K1, OR4K5 difficulties with 131,365,091 14q11.2 Gain 224,329 21,784,072- No/NS No known genes fine and gross 22,008,401 motor skills, 11q23: Multiple genes 15q11.2 Gain 1,662,280  18,427,103- No/S LOC283755, severe anxiety 109,979,883- 20,089,383 POTE15, attacks, not able 111,597,476 OR4M2, OR4N4 to relate to peers 22q11.22 Loss 515,645 21,031,117- No/NS PRAME, SUHW2, and is affected by 21,546,762 SUHW1, GGTL4 noise 22q11.23 Gain 269,129 23,975,202- No/S CTA, LRP5L 24,244,331 22 SK0145- Simplex family 46, XX, 7q31.2: No known genes 1p36.11 Gain 192,600 26,231,500- Yes/NS 8 genes Other 003 ASD t(7; 11)(q31; 114,573,150- 26,424,100 Canadian Family (67955) q25)mat 114,611,613 2p24.2 Gain  14,233 17,416,366- Yes/NS No known genes Apparently inherited 17,430,599 unaffected mother 11q25: No known genes 3p23 Gain  28,509 34,844,620- Yes/NS No known genes has the same 133,882,647- 34,873,129 7q31.2 and 11q25 134,001,155 5p15.33 Gain 3,029,476  165,712- Yes/NS 28 genes breakpoints 3,195,188 6p22.2 Gain  25,841 25,576,804- Yes/NS LRRC16 25,602,645 7p14.1 Gain  20,412 37,494,999- No/NS No known genes 37,515,411 8q13.3 Gain  28,933 72,911,162- Yes/NS MSC 72,940,095 10p12.1 Loss  98,961 27,642,965- No/S PTCHD3 27,741,926 12p12.3 Gain  37,831 18,855,833- No/NS No known genes 18,893,664 14q11.2 Gain 464,929 21,551,291- No/NS No known genes 22,016,220 15q23- Gain 435,603 70,053,228- Yes/NS 9 genes 24.1 70,488,831 19q13.43 Gain 308,600 63,476,500- Yes/NS 18 genes 63,785,100 23 SK0031- Simplex family 46, XY, 7q31.2: ST7 5p13.2 Loss  3,000 36,495,800- Yes/NS No known genes Other 003 ASD, very little t(7; 13)(q31.3; 116,270,156- 36,498,800 Non Canadian (68160L) language, global q21) mat 116,458,896 6p22.1- Gain  79,600 29,967,200- No/NS HLA-A Family developmental delays inherited 21.33 30,046,800 13q21.1: No known genes 9p23 Loss 112,800 11,895,600- No/NS No known genes 54,559,087- 12,008,400 54,739,454 14q32.2 Gain 772,400 99,015,100- Yes/S 8 genes 99,787,500 15q11.2 Gain 1,378,000  18,711,400- No/S LOC283755, 20,089,400 POTE15, OR4M2, OR4N4 17q21.31 Gain 597,300 41,569,000- No/NS 6 genes 42,166,300 22q11.23 Gain 251,200 23,989,000- No/S CTA-246H3.1, 24,240,200 LRP5L 24 SK0073- Simplex family 47, XX, 15q13: LOC400968, 1q25.2 Gain 424,000 176,522,000- Yes/NS 6 genes SK 003 ASD, developmental idic(15)q13) 28,918,525- LOC283755, 176,946,000 Described (57283L) delay, delayed de novo 31,848,963 POTE15, OR4M2, 2p23.3 Gain 703,500 24,701,300- Yes/NS 7 genes previously in expressive and OR4N4 . . . to . . . 25,404,800 Kwasnicka- receptive language ARHGAP11A, 4p16.3 Gain 997,460 1,692,240- Yes/NS 12 genes Crawford et al.⁴ c15orf45, 2,689,700 GREM1, RYR3 4q35.1 Gain 311,000 185,856,000- Yes/NS CASP3, 186,167,000 CCDC111, MLF1IP, ACSL1 5q31.1 Gain  93,000 134,426,000- Yes/S No known genes 134,519,000 9p21.1 Loss 362,900 30,452,800- Yes/NS No known genes 30,815,700 14q11.2 Gain 414,900 21,660,700- No/NS No known genes 22,075,600 15q11.2- Gain 11,922,600   18,376,200- Yes/S >50 genes 13.3 30,298,800 16p11.2 Gain 1,543,900  28,062,200- No/NS >20 genes 29,606,100 16p11.2 Gain 658,600 30,589,900- No/NS >20 genes 31,248,500 25 SK0218- Multiplex family 46, XX, 18q21.32: See CNV 12p13.33 Loss  92,328 1,760,084- Yes/S CACNA2D4, SK 003 ASD, cleft palate, del(18)(q21) 55,690,398- 1,852,412 ADIPOR2, As noted in the (60340) club feet, mild-facial de novo 55,884,029 LRTM2 Autism hypoplasia, heart 15q11.2 Loss 1,613,450  18,446,422- No/S LOC283755, Chromosome defect 20,059,872 POTE15, Rearrangment OR4M2, OR4N4 Database there 17q21.31 Gain 190,234 41,518,415- No/NS KIAA1267 are 5 addition 41,708,649 reported cases of 18q21.32- Loss 20,358,999   55,756,601- Yes/S >50 genes abnormalities q23 76,115,600 involving 18q; 19q13.42 Loss  68,786 59,971,717- No/NS KIR3DP1, Sibling has a 60,040,503 KIR2DL1, normal 46, XY KIR3DL1, karyotype also is KIR2DL4, affected with KIR2DS4 autism and has 20p11.23 Gain 128,457 19,740,012- Yes/NS RIN2 oromotor 19,868,469 difficulties. 26 SK0215- Simplex family 46, XY, 19p13.2: EVI5L, FLJ22184, 1p21.3 Loss 1,092,500  97,271,600- Yes/S FLJ35409, DPYD Other 006 ASD t(19; 21)(p13.2; 7,804,294- LRRC8E, MAP2K7, 98,364,100 Canadian Family (58449) q22.12) 7,896,711 SNAPC2, CTXN1 Patient has an inherited 21q22.12: No known genes 17p11.1- Gain 503,100 21,634,900- Yes/NS FAM27L unaffected sister 36,091,999- p11.2 22,138,000 with the same 36,191,098 karyotype 27 SK0136- Simplex family 46, X, Not available 4p13 Gain  42,400 44,809,500- No/NS No known genes 003 ASD der(Y)t(Y; 15) 44,851,900 (51253) (q12; p11.2) pat 8p23.2 Gain 234,580 2,335,310- No/NS No known genes inherited 2,569,890 8q24.23 Loss 138,000 137,757,000- No/NS No known genes SK 137,895,000 10p12.1 Loss  51,400 27,690,500- No/NS PTCHD3 27,741,900 15q11.2 Loss 558,300 18,676,700- No/NS LOC283755 19,235,000 15q26.3 Gain 388,100 99,827,900- No/NS PCSK6, TARSL2, 100,216,000 TM2D3, OR4F6 28 SK0243- Simplex Family 46, XY, See CNV See CNV 1q21.1 Loss 333,539 145,700,996- No/NS No known genes 003 ASD del(15)(q23q24.2) 146,034,535 (67941) de novo 2p22.2 Gain  52,951 37,847,789- No/NS No known genes SK 37,900,740 3q27.3 Gain  91,422 187,897,578- No/S KNG1, EIF4A2 187,989,000 7p22.3 Gain  29,778 141,322- No/NS No known genes 171,100 7p14.1 Loss  32,636 38,092,579- No/NS No known genes 38,125,215 10p13 Loss  1,570 13,096,593- No/NS No known genes 13,098,163 11p15.1 Gain  21,766 18,905,796- No/NS MRGPRX1 18,927,562 15q23- Loss 4,289,500  69,601,300- Yes/S 55 genes q24.2 73,890,800 17q12 Gain  38,247 31,463,252- No/NS No known genes 31,501,499 17q21.31 Gain  83,359 41,636,474- No/NS No known genes 41,719,833 29 SK0245- Simplex Family 46, XY, See CNV See CNV 6q14.1 Loss  47,288 79,036,117- No/NS No known genes 005 ASD, epicanthal trp(15)(q11.2q13) 79,083,405 (68517) folds, drooping eyes de novo 7p14.1 Loss  57,861 38,067,354- No/NS No known genes SK 38,125,215 10p13 Loss  2,538 13,095,625- No/NS TARP 13,098,163 11p15.1 Loss  12,459 18,905,796- No/NS MRGPRX1 18,918,255 14q11.2 Loss 219,458 19,272,965- No/S 6 genes 19,492,423 14q32.33 Gain  27,408 106,223,861 No/NS No known genes 106,251,269 15q11.2- Gain 11,871,747   18,427,100 Yes/S >50 genes q13.3 30,298,847 19p13.2 Loss 132,251 6,902,567 No/S EMR4, 7,034,818 FLG25758, MBD3L2, ZF557 30 NA0097- Simplex Family 46, XX, 11q23: not 2p25.3- Gain 63,451,406^(b)   2,994 Yes/S >50 genes NFLD 000 ASD t(11; 12)(q23.3; available 2p15 63,454,400 (82361L) p13.3) 3p24.2 Loss 159,273 25,980,400- No/NS No known genes unknown 26,139,673 12p11.21 Gain 236,006 31,065,545- No/S DDX11, OVOS2 31,301,551 12p13.32-p13.31: Multiple genes 14q11.2 Gain 489,269 21,498,204 No/NS No known genes 4,341,718- 21,987,473 7,918,138 Xp22.33- Loss 5,825,311  34,419- Yes/S 21 genes Xp22.31 5,859,730 31 SK0300- Multiplex Family 46, X, Not available 4p16.1 Gain  35,832 7,801,488- Yes/NS SORCS2 003 ASD, NF1 inv(Y) 7,837,320 (77447) (p11.2q11.2)pat 5p15.33 Gain 124,630 752,190- No/S ZDHHC11 inherited 876,820 6p25.1 Loss 215,567 4,200,904- Yes/S No known genes SK 4,416,471 8q24.23 Loss 198,193 137,757,137- No/S No known genes 137,955,330 11p15.4 Loss  54,390 6,845,440- Yes/S OR10A2, 6,899,830 OR10A4, OR2D2, OR2D3 14q11.2 Loss 229,676 19,272,965- No/NS 6 genes 19,502,641 15q11.2 Loss 1,908,356  18,427,103- No/S LOC283755, 20,335,459 POTE15, Error! OR4M2, OR4N4 Hyperlink reference not valid. 15q21.2 Gain 183,903 48,583,127- Yes/S TRPM7, USP50 48,767,030 Xp11.23 Loss  83,750 47,643,250- No/S ZNF630, SSX6 47,727,000 32 SK0094- Multiplex Family 46, XX, Not available 7q21.2 Loss 509,800 90,919,200- Yes/NS MTERF, AKAP9, SK 005 ASD ins(21; ?)(p11.2; ?) 91,429,000 CYP51A1, (49304) unknown LOC401387 9q32 Gain 211,000 112,463,000- No/NS KIAA1958, 112,674,000 C9orf80 10q11.22 Gain 124,800 47,030,100- No/NS No known genes 47,154,900 14q32.33 Gain 186,000 105,829,000- No/NS No known genes 106,015,000 Xq23 Loss 888,000 112,325,000- Yes/NS No known genes 113,213,000

Affymetrix GeneChip Human Mapping 500K Array Set

For each sample, approximately 500,000 SNPs were genotyped using the combined two-chip Nspl and Styl GeneChip® Human Mapping Commercial or Early Access Arrays (Affymetrix, Inc., Santa Clara, Calif.) according to the manufacturer's instructions and as described previously (Kennedy et al. 2003 Nat Biotechnol. 21:1233-7, the contents of which are incorporated herein by reference). Briefly, 250 ng of genomic DNA was digested with Nspl and Styl restriction enzyme (New England Biolabs, Boston, Mass.), ligated to an adaptor and amplified by PCR. The PCR products were then fragmented with DNaseI to a size range of 250 bp to 2,000 bp, labelled, and hybridized to the array. After hybridization, arrays were washed on the Affymetrix fluidics stations, stained, and scanned using the Gene Chip Scanner 3000 7G and Gene Chip Operating System. Data has been submitted to the Gene Expression Omnibus database (accession GSE9222). Karyotypes were generated using standard clinical diagnostic protocols.

Characterization of Copy Number Variation

Nspl and Styl array scans were analyzed for copy number variation using a combination of DNA Chip Analyzer (dChip) (Li and Wong 2001 Genome Biology 2: 0032.1-0032.11), Copy Number Analysis for GeneChip (CNAG) (Nannya 2005 Cancer Res. 65:6071-9) and Genotyping Microarray based CNV Analysis (GEMCA) (Komura 2006 Genome Res. 16:1575-84). Each of these references is incorporated herein by reference.

Analysis with dChip (www.dchip.org) was performed as previously described (Zhao et al 2005 Cancer Res. 65:5561-70) in batches of ˜100 probands. Briefly, array scans were normalized at the probe intensity level with an invariant set normalization method. After normalization, a signal value was calculated for each SNP using a model-based (PM/MM) method. In this approach, image artifacts were identified and eliminated by an outlier detection algorithm. For both sets of arrays, the resulting signal values were averaged across all samples for each SNP to obtain the mean signal of a diploid genome. From the raw copy numbers, the inferred copy number at each SNP was estimated using a Hidden Markov Model (HMM).

For analyses with CNAG version 2.0 (www.genome.umin.jp), the reference pool was set to include all samples and performed an automatic batch pair-wise analysis using sex-matched controls. Test samples were compared to all samples within the reference pool and matched based on signal intensity standard deviations. The scan intensities for each ‘test’ sample were compared to the average intensities of the reference samples (typically the average of 5-12 samples) and used to calculate raw copy number changes. Underlying copy number changes were then inferred using a Hidden Markov Model (HMM) built into CNAG.

GEMCA analysis was performed essentially as described (Komura et al. Genome Res 2006; 16(12):1575-84) with the exception that two designated DNA samples (NA10851 and NA15510) were used as references for pair-wise comparison to all proband experiments. These results were further filtered by only including those CNVs that were common to both pair-wise experiments.

CNVs were merged if they were detected in the same individual by more than one algorithm using the outside probe boundaries.

Controls and Autism Chromosome Rearrangement Database (ACRD)

Control samples consisted of (i) CNVs observed in 500 Europeans from the from the German PopGen project (Krawczak et al. Community Genet 2006; 9(1):55-61), and CNVs found in a cohort of 1000 Caucasian non-disease controls from the Ontario population (ref. 24). The ACRD that had 834 putative CNVs or breakpoints mapped to the genome was established. A CNV was considered ASD-specific if it was >10 kb, contained at least three probes and at least 20% of its total length was unique when compared to controls.

CNV Validation Experiments and Balance Rearrangement Breakpoint Mapping

PCR validation of CNV calls was performed using Quantitative Multiplex PCR of short fluorescent fragments (QMPSF) (Redon et al. Nature. 444:444-54) or SYBR-Green 1 based real-time quantitative PCR (qPCR) using controls at the ACCN1, CFTR or FOXP2 loci (PMID: 14552656). For both methods, primers were designed using the program PRIMER3 (http://frodo.wi.mit.edu/). Balanced rearrangements were mapped primarily using FISH (Nannya et al. Cancer Res 2005; 65(14):6071-9). The microdel program (Komura et al., ibid) was used to score CNV losses.

For QMPSF, short genomic sequences (140-220 bp) within putative CNVs were PCR amplified using dye-labelled primers corresponding to unique sequences. Each reaction also included co-amplified control amplicons corresponding to either ACCN1 or CFTR located at 17q11.2 and 7q31.2, respectively. Briefly, 40 ng of genomic DNA was amplified by PCR in a final volume of 25 μl using AmpliTaq® DNA polymerase (manufactured for Applied Biosystems by Roche Molecular Systems, Inc.) After an initial step of denaturation at 95° C. for 5 minutes conditions were as follows: 25 PCR cycles of 94° C. for 30 seconds, annealing at 60° C. for 45 seconds, and extension at 72° C. for 30 seconds. A final extension step at 72° C. for 15 minutes followed. QMPSF amplicons were separated on an ABI 3730xl DNA Analyzer (Applied Biosystems, Foster City, Calif.), and analyzed using ABI GeneMapper® software version 3.7 (Applied Biosystems). After adjustment of control amplicons to the same heights, the QMPSF pattern generated from test DNA was superimposed to that of the control DNA. For each putative CNV locus, the copy number ratio was determined by dividing the normalized peak height obtained from the test DNA by that of the control DNA. Peak ratios of >1.4 and <0.7 were indicative of copy number gains and losses, respectively. At least two independent QMPSF assays were required for CNV confirmation.

SYBR Green 1-based real-time qPCR amplification was performed using a Mx3005P quantitative PCR system (Stratagene, La Jolla, USA). Non-fluorescent primers were designed to amplify short genomic fragments (<140 bp) in putative CNV loci. Each assay also included amplification of a control amplicon corresponding to FOXP2 at 7q31.1 for comparison. After optimization of primer sets with control genomic DNA using ‘Brilliant® SYBR® Green QPCR Master Mix’ (Stratagene), test samples were assayed in 15 μl reaction mixtures in 96-well plates containing: 7.5 μl of reaction mix, 1.8 μl of primer, 6.0 ng of genomic DNA at 1.2 ng/μl, 0.225 μl of reference dye with 1:500 dilution, and 0.475 μl of water. PCR conditions consisted of 10 minutes of polymerase activation at 95° C., followed by 40 cycles of: 95° C. for 15 seconds and a single step at 60° C. for 1 minute for annealing and elongation. These steps were then followed by a final cycle of 95° C. for 1 minute, 55° C. for 30 seconds, and 95° C. for 30 seconds. Standard curve quantification was analyzed by MxPro-Mx3005P software (version 3.20 Build 340) to calculate copy number changes. Coefficient of variation (CV) was calculated on all sample Ct values to remove possible outlier when CV was greater than 1%. The average quantity of the putative CNV locus was divided by the average quantity of the control amplicon on FOXP2. Ratios of >1.4 and <0.7 were indicative of copy number gains and losses, respectively. Each putative CNV locus had at least two independent assays.

Results Structural Variation Characteristics in ASD Cases

A total of 426 ASD index cases were tested for CNV content including 394 typical idiopathic cases and 32 others that were enrolled based on prior knowledge of having a cytogenetic abnormality. The Affymetrix 500 k SNP array was used because it provided the highest resolution screen available for both SNP genotype and CNV data. Using the SNPs, the ancestry of each sample was categorized (to guide selection of controls). Backgrounds of the samples were found to be: 90.3%, 4.5%, 4.5%, and 0.7%, European, European/mixed, Asian, or Yoruban, respectively.

To maximize CNV discovery, three calling algorithms were used as described above (see FIG. 1) and common results between them were merged to identify a ‘full’ dataset of 3389 independent CNVs (˜8 CNVs per genome, mean size 390 kb) (see Table 4 below). To minimize potential false positives, a second dataset was generated whereby a CNV needed to be detected by two or more algorithms and/or on both the NspI or StyI microarrays (Pinto et al. Hum Mol Genet 2007; 16 Spec No 2:R168-73).

This ‘stringent’ dataset contained 1312 CNVs (˜3 CNVs per genome, mean size 603 kb). Using q-PCR, 48% (12/26) and 96% (48/50) of random CNVs were validated in the full and stringent collections, respectively.

TABLE 4 Summary of CNV in ASD and Controls POPGEN CONTROLS AUTISM PROBANDS All CNVs All CNVs Autism Specific¹ Full Stringent² Full Stringent² Full Stringent² #samples 500 500 426 426 426 426 #CNVs 3695 1558 3389 1312 888 276 CNV/Genome³ 7.4 3.1 8.0 3.1 2.1 0.65 Mean/Median 315/151 470/224 390/162 603/219 518/121 1082/194   Size (kb) % Gain/Loss  59/41%  70/30%  58/42%  62/38%  61/39% 57/43% Overlapping 3005/333 (81%) 1226/142 (78%) 2728/277 (80%) 980/94 (74%) 397/122 (44%) 30/13 (11%) CNV/Loci (%)⁴ >1 Mb CNV (%) 343 (9%) 250 (16%) 339 (10%) 212 (16%) 63 (7%) 32 (12%) ¹Not seen in controls. ²Stringent dataset as called by >1 algorithms or arrays. Analysis with dChip was performed in batches of ~100 probands. For CNAG version 2.0, the reference pool was set to include all samples and performed an automatic batch pairwise analysis using sex-matched controls. For GEMCA two designated DNA samples (NA10851 and NA15510) were used as references for pairwise comparison to all proband experiments. These results were further filtered by only including those CNVs that were common to both pairwise experiments. In all instances CNVs were merged if they were detected in the same individual by more than one algorithm using the outside probe boundaries. ³CNV/genome breakdown by algorithm: dChip Merged (3.0/genome), CNAG Merged (5.6/genome), GEMCA (5.5/genome). Validation experiments using q-PCR and FISH are described in the text. Another form of validation comes from examining the trios where we can demonstrate inheritance in 48 (maternal is 25, paternal is 23) of the autism-specific stringent dataset. Also from the trios, 148 confirmed regions (inheritance assignment) in the stringent dataset that overlap with controls (maternal is 65, paternal is 83). ⁴Represents the total number of overlapping and/or recurrent CNVs, the number of overlapping/CNV loci, and the percentage of overlapping CNVs, out of the total dataset.

Five hundred European control samples were examined for their CNV content and similar numbers of CNVs (3695 in the full and 1558 in the stringent dataset) were found to those in the ASD cases (Table 4). This suggested germ-line chromosome instability was not a significant contributing mechanism. The ASD CNVs were then compared against the 500 European/Caucasian controls and the Database of Genomic Variants (a repository of structural variation in ‘non-disease’ populations) (Iafrate et al. Nat Genet 2004; 36(9):949-51) to establish autism-specific CNV datasets. The subsequent analysis then focused on the 276 CNVs in the stringent autism-specific category, which mapped across all 23 chromosomes (FIG. 2), details of which are found in Table 3, below. Additional ASD-relevant CNV data is also found in the other categories in Table 5 (discussed below).

TABLE 3 FAM ID (DNA) Sex Type Chr start stop size CNV CNV Category SK0215-006 (58449) M CHR 1 97,271,600 98,364,100 1,092,500  loss CNVs confirmed de novo SK0152-003 (41548L) M CHR 3 15,125,800 16,535,400 1,409,600  loss CNVs confirmed de novo SK0181-003 (52191) M CHR 3 65,286,300 70,633,200 5,346,900  loss CNVs confirmed de novo SK0205-004 (56242) F CHR 5   81,949 13,882,933 13,800,984   loss CNVs confirmed de novo SK0152-003 (41548L) M CHR 5  9,275,811 12,705,200 3,429,389  loss CNVs confirmed de novo SK0083-003 (50800L) M CHR 7 108,200,381  119,223,887  11,023,507   loss CNVs confirmed de novo SK0131-003 (39989) F CHR 7 113,335,000  128,821,721  15,486,722   loss CNVs confirmed de novo SK0262-003 (68609) M SPX 8   710,491  1,501,580 791,089 gain CNVs confirmed de novo SK0152-003 (41548L) M CHR 12  40,584,198 41,007,040 422,842 loss CNVs confirmed de novo MM0278-003 (57788) M SPX 12  114,170,000  132,388,000  18,218,001   gain CNVs confirmed de novo SK0243-003 (67941) M CHR 15  69,601,300 73,890,800 4,289,500  loss CNVs confirmed de novo NA0067-000 (65344L) M SPX 16  87,800,593 88,066,260 265,668 loss CNVs confirmed de novo SK0218-003 (60340) F CHR 18  55,756,601 76,115,600 20,358,999   loss CNVs confirmed de novo MM0109-003 (46486) F SPX 20  60,949,339 62,377,000 1,427,662  gain CNVs confirmed de novo SK0244-003 (69183) M SPX 21  42,974,148 43,328,084 353,936 gain CNVs confirmed de novo NA0039-000 (69736) F CHR 22  46,277,400 49,509,100 3,231,700  loss CNVs confirmed de novo MM0109-003 (46486) F SPX 22  49,243,247 49,519,949 276,703 loss CNVs confirmed de novo NA0097-000 (82361L) F CHR X   34,419  5,859,730 5,825,312  loss CNVs confirmed de novo SK0306-004 (78681) F SPX X 48,073,600 52,716,966 4,643,367  gain CNVs confirmed de novo SK0147-003 (47544L) F SPX 2 114,855,796  115,334,166  478,371 loss CNVs Recurrent/Overlapping SK0167-003 (60966L) F MPX 2 114,855,796  115,334,166  478,371 gain CNVs Recurrent/Overlapping SK0288-003 (75420) F SPX-MZ 2 115,141,880  115,247,000  105,121 gain CNVs Recurrent/Overlapping NA0030-000 (55240) M SPX 2 186,674,000  186,786,323  112,324 loss CNVs Recurrent/Overlapping SK0306-004 (78681) F SPX 2 186,674,000  186,771,130   97,131 loss CNVs Recurrent/Overlapping MM0220-003 (61180L) M MPX 6 118,799,000  119,117,000  318,001 gain CNVs Recurrent/Overlapping NA0025-000 (60490) M SPX 6 118,823,011  119,117,000  293,990 gain CNVs Recurrent/Overlapping SK0190-003 (54742) M SPX 7 152,698,000  154,478,000  1,780,000  gain CNVs Recurrent/Overlapping SK0115-003 (40555) M SPX 7 153,098,000  153,372,000  274,001 gain CNVs Recurrent/Overlapping SK0058-003 (59963) M MPX 7 153,539,745  153,556,533   16,789 gain CNVs Recurrent/Overlapping SK0143-003 (36812) M SPX 8 53,481,200 53,766,400 285,201 gain CNVs Recurrent/Overlapping MM0236-004 (46475) M MPX 8 53,724,445 53,996,124 271,680 gain CNVs Recurrent/Overlapping SK0270-003 (71341) M SPX 9  7,725,280  7,764,180  38,900 loss CNVs Recurrent/Overlapping MM0103-003 (42387) M MPX 9  7,725,283  7,760,233  34,951 loss CNVs Recurrent/Overlapping MM0272-003 (45563) M MPX 11  40,285,800 40,548,738 262,939 loss CNVs Recurrent/Overlapping SK0167-003 (60966L) F MPX 11  40,417,554 40,610,400 192,847 loss CNVs Recurrent/Overlapping SK0023-003 (58096) M SPX 13  66,470,851 66,660,289 189,438 gain CNVs Recurrent/Overlapping MM0299-003 (51674) F MPX 13  66,487,899 66,660,300 172,402 gain CNVs Recurrent/Overlapping MM0109-003 (46486) F SPX 16  21,441,805 22,688,093 1,246,289  gain CNVs Recurrent/Overlapping MM0289-003 (42267) F MPX 16  21,808,808 22,611,363 802,556 loss CNVs Recurrent/Overlapping MM0088-003 (45562) F MPX 16  29,559,989 30,235,818 675,830 loss CNVs Recurrent/Overlapping NA0133-000 (78119L) F SPX 16  29,559,989 30,085,308 525,320 gain CNVs Recurrent/Overlapping SK0091-004 (46407) F MPX 22  17,265,500 21,546,762 4,281,262  gain CNVs Recurrent/Overlapping SK0323-003 (80022) M MPX 22  18,683,900 19,427,000 743,101 gain CNVs Recurrent/Overlapping SK0123-004 (60536L) M MPX 22  47,717,300 48,318,828 601,528 gain CNVs Recurrent/Overlapping MM0102-003 (47598) M MPX 22  48,152,289 48,232,669  80,380 loss CNVs Recurrent/Overlapping NA0002-000 (52026) M SPX 7 153,585,000  153,651,462   66,463 loss CNVs Recurrent/Overlapping/ CNVs confirmed de novo SK0073-003 (57283L) F CHR 15  18,376,200 30,298,800 11,922,600   gain CNVs Recurrent/Overlapping/ CNVs confirmed de novo SK0245-005 (68517) M CHR 15  18,427,100 30,298,847 11,871,747   gain CNVs Recurrent/Overlapping/ CNVs confirmed de novo SK0119-003 (35190) M MPX 22  17,014,900 19,786,200 2,771,300  loss CNVs Recurrent/Overlapping/ CNVs confirmed de novo SK0297-003 (76066) M SPX-MZ 22  17,265,500 21,546,762 4,281,263  gain CNVs Recurrent/Overlapping/ CNVs confirmed de novo MM0109-003 (46486) F SPX 17  40,555,289 41,089,766 534,478 loss CNVs that are Singletons MM0240-003 (43743) F MPX 17  40,555,289 41,128,323 573,035 loss CNVs that are Singletons NA0074-000 (63358) M SPX 1 41,463,611 41,924,314 460,704 gain CNVs that are Singletons SK0036-003 (29186) F SPX 1 57,936,233 58,514,629 578,396 gain CNVs that are Singletons MM0236-004 (46475) M MPX 1 60,369,200 61,426,300 1,057,101  gain CNVs that are Singletons MM0020-004 (47838) M MPX 1 65,649,086 65,713,423  64,338 gain CNVs that are Singletons NA0076-000 (63624) M SPX 1 91,930,266 92,330,344 400,078 gain CNVs that are Singletons SK0174-003 (64379L) M SPX 1 108,046,000  108,246,283  200,284 loss CNVs that are Singletons SK0283-003 (72309) F CHR 1 148,095,537  149,547,463  1,451,926  gain CNVs that are Singletons MM0011-003 (60566L) M MPX 1 165,908,677  166,028,402  119,726 loss CNVs that are Singletons SK0132-003 (30661) M MPX 1 186,673,899  186,716,570   42,672 loss CNVs that are Singletons NA0109-000 (72873) M SPX 1 212,037,558  212,471,000  433,443 loss CNVs that are Singletons SK0183-004 (52217) M SPX 1 238,633,145  239,606,926  973,781 loss CNVs that are Singletons MM0219-003 (46823) M MPX 2 34,155,700 34,253,221  97,522 loss CNVs that are Singletons MM0295-003 (46488) M MPX 2 34,662,196 34,780,515 118,320 loss CNVs that are Singletons NA0083-000 (66104L) M SPX 2 34,858,330 34,937,455  79,125 loss CNVs that are Singletons SK0270-003 (71341) M SPX 2 39,992,374 40,053,300  60,926 loss CNVs that are Singletons NA0055-000 (59448) M SPX 2 41,958,200 42,088,448 130,249 loss CNVs that are Singletons SK0301-003 (77203) M MPX 2 52,856,046 52,969,575 113,530 loss CNVs that are Singletons NA0027-000 (60421L) M MPX 2 121,623,000  121,684,915   61,915 loss CNVs that are Singletons NA0057-000 (59537) M SPX 2 125,496,832  125,890,571  393,740 loss CNVs that are Singletons MM0176-003 (62118L) M MPX 2 135,358,000  135,471,070  113,071 loss CNVs that are Singletons SK0225-003 (60921) M SPX 2 155,849,451  155,988,560  139,109 loss CNVs that are Singletons SK0192-003 (54877) M SPX 2 181,771,621  181,944,065  172,445 loss CNVs that are Singletons NA0007-000 (50611) M SPX 2 195,170,000  195,217,247   47,248 gain CNVs that are Singletons SK0283-003 (72309) F CHR 3  5,365,506  5,409,964  44,458 loss CNVs that are Singletons MM0210-004 (47376) M MPX 3  7,957,390  8,250,541 293,151 gain CNVs that are Singletons NA0044-000 (57097) M SPX 3 35,613,300 35,928,200 314,901 gain CNVs that are Singletons SK0021-008 (51504) M MPX 3 36,110,965 36,215,909 104,945 loss CNVs that are Singletons MM0154-003 (56678L) F MPX 3 50,089,500 50,199,200 109,701 gain CNVs that are Singletons SK0152-003 (41548L) M CHR 3 78,902,000 78,957,000  55,000 gain CNVs that are Singletons NA0044-000 (57097) M SPX 3 82,866,400 84,544,763 1,678,364  gain CNVs that are Singletons SK0023-003 (58096) M SPX 3 99,400,957 99,484,400  83,443 gain CNVs that are Singletons NA0018-000 (72622) M SPX 3 117,838,700  117,937,000   98,301 gain CNVs that are Singletons NA0003-000 (48474) M SPX 3 124,386,373  124,456,000   69,628 gain CNVs that are Singletons NA0090-000 (65410) M SPX 3 183,837,706  183,940,069  102,364 gain CNVs that are Singletons NA0044-000 (57097) M SPX 4 55,718,164 55,811,710  93,547 loss CNVs that are Singletons NA0016-000 (51524L) F SPX 4 114,333,509  114,416,051   82,542 loss CNVs that are Singletons SK0012-003 (58468L) M SPX 4 152,993,000  153,381,007  388,008 gain CNVs that are Singletons SK0103-005 (42258) M SPX 4 157,615,000  157,683,000   68,000 gain CNVs that are Singletons NA0037-000 (69812) M SPX 4 179,692,000  179,865,679  173,680 gain CNVs that are Singletons MM0299-003 (51674) F MPX 4 181,968,784  182,095,665  126,882 loss CNVs that are Singletons SK0266-003 (68257) M SPX 4 183,466,000  183,517,000   51,000 loss CNVs that are Singletons SK0002-003 (50002) F CHR 5 14,940,400 15,179,500 239,100 gain CNVs that are Singletons NA0078-000 (63727) M MPX 5 25,125,371 25,450,672 325,302 gain CNVs that are Singletons NA0076-000 (63624) M SPX 5 37,409,881 37,778,834 368,953 gain CNVs that are Singletons SK0335-003 (72815) F CHR 5 38,534,384 38,807,002 272,619 loss CNVs that are Singletons MM0143-004 (47386) M MPX 5 110,440,484  110,471,180   30,697 gain CNVs that are Singletons NA0023-000 (60504L) F SPX 5 113,104,916  113,178,000   73,084 loss CNVs that are Singletons SK0118-003 (52027) M SPX 5 122,834,399  123,029,036  194,638 loss CNVs that are Singletons SK0077-003 (48226) M SPX 5 128,968,799  129,433,000  464,201 gain CNVs that are Singletons SK0300-003 (77447) M CHR 6  4,200,904  4,416,471 215,568 loss CNVs that are Singletons MM0212-004 (62223L) F MPX 6 17,505,095 17,703,208 198,114 gain CNVs that are Singletons MM0300-003 (47836) F MPX 6 27,827,354 28,119,631 292,278 gain CNVs that are Singletons MM0225-004 (60826) M MPX 6 69,929,900 70,278,043 348,144 gain CNVs that are Singletons SK0217-003 (59279) M SPX 6 112,679,982  112,776,094   96,112 gain CNVs that are Singletons SK0326-003 (81155) M SPX 6 137,930,847  138,011,644   80,798 gain CNVs that are Singletons MM0088-003 (45562) F MPX 7  2,922,139  2,964,895  42,757 loss CNVs that are Singletons NA0147-000 (77123L) M SPX 7  3,946,854  4,002,686  55,833 loss CNVs that are Singletons SK0049-004 (59987L) M MPX 7 11,526,500 11,560,300  33,800 gain CNVs that are Singletons SK0132-003 (30661) M MPX 7 20,242,925 20,345,800 102,876 gain CNVs that are Singletons NA0145-000 (82058L) M SPX 7 47,742,927 48,775,200 1,032,274  loss CNVs that are Singletons SK0119-003 (35190) M MPX 8 17,706,313 17,738,524  32,211 loss CNVs that are Singletons SK0262-003 (68609) M SPX 8 18,623,000 19,442,500 819,500 gain CNVs that are Singletons SK0077-003 (48226) M SPX 8 42,971,601 43,820,300 848,699 gain CNVs that are Singletons SK0294-003 (76222) M SPX 8 73,762,894 73,798,241  35,348 gain CNVs that are Singletons SK0076-003 (38712) F SPX 8 83,989,256 84,141,278 152,022 gain CNVs that are Singletons MM0241-004 (45547) M MPX 8 87,230,811 87,498,988 268,178 gain CNVs that are Singletons MM0210-004 (47376) M MPX 8 104,166,572  104,947,190  780,618 gain CNVs that are Singletons SK0194-003 (55078) M SPX 8 123,539,127  123,644,422  105,296 loss CNVs that are Singletons SK0292-003 (75896) F MPX 8 130,467,000  130,529,193   62,194 loss CNVs that are Singletons MM0007-003 (59978) M MPX 9  5,099,530  5,235,490 135,961 gain CNVs that are Singletons MM0711-003 (63583L) M MPX 9 16,092,066 16,379,100 287,035 gain CNVs that are Singletons SK0015-003 (49932) M MPX 9 19,284,100 19,511,500 227,400 gain CNVs that are Singletons SK0015-003 (49932) M MPX 9 19,702,200 24,674,100 4,971,900  loss CNVs that are Singletons SK0278-003 (74431) M SPX 9 22,626,541 22,747,714 121,174 loss CNVs that are Singletons SK0148-005 (41350) F SPX 9 24,607,036 24,682,114  75,078 loss CNVs that are Singletons MM0020-004 (47838) M MPX 9 25,439,100 25,535,000  95,901 loss CNVs that are Singletons NA0105-000 (72085) M SPX 9 33,054,336 33,294,800 240,465 gain CNVs that are Singletons NA0147-000 (77123L) M SPX 9 84,957,060 85,054,672  97,613 loss CNVs that are Singletons SK0045-003 (58937) M MPX 9 109,446,000  109,837,000  391,000 gain CNVs that are Singletons MM0117-003 (59983) M MPX 10   2,313,505  2,407,102  93,598 loss CNVs that are Singletons MM0225-004 (60826) M MPX 10   4,976,040  5,124,511 148,472 gain CNVs that are Singletons MM1086-004 (76285) M MPX 10  31,256,118 31,604,509 348,392 loss CNVs that are Singletons MM0068-003 (60836) M MPX 10  68,139,200 68,246,027 106,828 loss CNVs that are Singletons NA0037-000 (69812) M SPX 10  104,641,000  104,786,777  145,778 loss CNVs that are Singletons SK0300-003 (77447) M CHR 11   6,845,440  6,899,830  54,391 loss CNVs that are Singletons SK0322-003 (79950) M SPX 11  33,159,190 33,462,070 302,881 gain CNVs that are Singletons MM0305-003 (47607) M MPX 11  68,053,777 68,204,900 151,123 gain CNVs that are Singletons NA0032-000 (55186) M SPX 11  76,114,600 76,140,500  25,900 gain CNVs that are Singletons MM0212-004 (62223L) F MPX 11  99,148,202 99,289,243 141,042 loss CNVs that are Singletons SK0167-003 (60966L) F MPX 11  101,131,785  101,246,901  115,117 loss CNVs that are Singletons MM0112-005 (46736) M MPX 11  116,789,980  116,855,347   65,368 gain CNVs that are Singletons MM0240-003 (43743) F MPX 11  117,452,000  117,539,000   87,001 gain CNVs that are Singletons SK0255-003 (68785) M SPX 11  124,303,460  124,719,976  416,517 gain CNVs that are Singletons NA0065-000 (62798L) M SPX 11  125,639,908  126,102,027  462,120 gain CNVs that are Singletons NA0172-000 (80993L) M SPX 12   3,727,911  3,879,230 151,320 loss CNVs that are Singletons SK0059-003 (29224) M SPX 12  10,431,082 10,445,300  14,218 gain CNVs that are Singletons SK0326-003 (81155) M SPX 12  46,170,200 46,365,774 195,575 gain CNVs that are Singletons SK0110-003 (24626) M SPX 12  50,520,400 50,573,516  53,116 gain CNVs that are Singletons NA0071-000 (64719L) F SPX 12  57,408,270 58,532,356 1,124,087  gain CNVs that are Singletons SK0305-003 (78621) F SPX 12  77,239,265 77,364,400 125,136 loss CNVs that are Singletons SK0301-003 (77203) M MPX 12  83,388,935 83,428,800  39,866 gain CNVs that are Singletons NA0093-000 (66999) M SPX 12  96,496,784 96,568,500  71,716 loss CNVs that are Singletons MM0711-003 (63583L) M MPX 12  96,576,486 96,639,686  63,201 loss CNVs that are Singletons SK0292-003 (75896) F MPX 12  101,568,000  101,586,000   18,001 gain CNVs that are Singletons NA0109-000 (72873) M SPX 12  110,646,607  110,800,000  153,394 gain CNVs that are Singletons MM0210-004 (47376) M MPX 12  125,446,000  125,757,000  311,000 gain CNVs that are Singletons SK0079-003 (48388) M MPX 13  17,960,300 18,492,994 532,694 gain CNVs that are Singletons NA0028-000 (58891L) M SPX 13  62,915,912 62,977,748  61,837 loss CNVs that are Singletons SK0326-003 (81155) M SPX 13  89,726,966 90,134,219 407,254 gain CNVs that are Singletons NA0048-000 (58569) M SPX 13  93,288,520 93,344,600  56,081 gain CNVs that are Singletons SK0326-003 (81155) M SPX 13  93,497,400 93,732,931 235,532 gain CNVs that are Singletons SK0254-003 (68687) M SPX 13  105,172,000  105,357,000  185,000 gain CNVs that are Singletons SK0121-003 (41288) M SPX 14  76,007,842 76,924,400 916,558 gain CNVs that are Singletons SK0031-003 (68160L) M CHR 14  99,015,100 99,787,500 772,400 gain CNVs that are Singletons SK0300-003 (77447) M CHR 15  48,583,127 48,767,030 183,904 gain CNVs that are Singletons SK0326-003 (81155) M SPX 15  97,406,000 97,961,522 555,523 gain CNVs that are Singletons SK0281-003 (72934) M SPX 16  57,542,779 57,579,900  37,122 loss CNVs that are Singletons MM0310-005 (60951) M MPX 16  80,972,252 80,983,135  10,884 loss CNVs that are Singletons SK0203-004 (56040) M MPX 16  82,603,600 82,687,900  84,300 gain CNVs that are Singletons SK0085-004 (30422) M MPX 17   3,836,592  3,998,867 162,276 gain CNVs that are Singletons SK0298-003 (77697) M SPX 17  76,914,079 77,771,141 857,063 gain CNVs that are Singletons SK0328-003 (82302) M SPX 18  13,794,043 14,743,900 949,858 gain CNVs that are Singletons SK0303-003 (78391) F MPX 18  28,383,551 28,448,100  64,550 loss CNVs that are Singletons SK0014-003 (41606) M SPX 18  52,531,252 53,165,421 634,169 gain CNVs that are Singletons SK0121-003 (41288) M SPX 19  33,693,363 33,762,805  69,442 loss CNVs that are Singletons NA0111-000 (73891) M SPX 19  57,836,600 58,246,200 409,601 gain CNVs that are Singletons NA0004-000 (47490) M SPX 19  58,634,965 58,958,584 323,620 gain CNVs that are Singletons NA0070-000 (64249L) F SPX 19  60,499,398 60,742,656 243,259 loss CNVs that are Singletons SK0047-003 (47173L) F SPX 19  61,910,800 62,644,900 734,100 loss CNVs that are Singletons NA0110-000 (72165) M SPX 19  63,050,356 63,193,800 143,445 loss CNVs that are Singletons SK0232-003 (59838) M MPX 19  63,483,000 63,771,100 288,100 gain CNVs that are Singletons MM0018-003 (59980) M MPX 20  11,319,093 11,424,900 105,808 loss CNVs that are Singletons SK0335-003 (72815) F CHR 20  14,955,730 15,011,214  55,485 loss CNVs that are Singletons SK0258-004 (67930) M SPX 20  45,468,000 45,673,300 205,300 gain CNVs that are Singletons MM0126-003 (54581) M MPX 21  22,839,570 22,938,377  98,808 loss CNVs that are Singletons SK0118-003 (52027) M SPX 21  28,060,406 28,250,400 189,995 loss CNVs that are Singletons SK0186-004 (52964) M SPX X 22,962,800 23,119,000 156,200 loss CNVs that are Singletons MM0087-003 (59962L) M MPX X 25,516,263 25,620,400 104,138 loss CNVs that are Singletons NA0100-000 (70601L) M SPX X 44,395,900 45,060,800 664,901 gain CNVs that are Singletons SK0087-003 (60692L) F MPX X 83,866,300 92,175,100 8,308,800  loss CNVs that are Singletons MM0020-004 (47838) M MPX X 87,452,050 87,595,200 143,151 gain CNVs that are Singletons SK0228-003 (62083) M SPX X 104,153,000  104,638,000  485,000 gain CNVs that are Singletons SK0088-003 (64798) M SPX X 114,042,922  114,215,435  172,513 gain CNVs that are Singletons MM0087-003 (59962L) M MPX X 130,406,000  130,695,499  289,500 gain CNVs that are Singletons NA0016-000 (51524L) F SPX X 140,600,370  140,907,495  307,125 gain CNVs that are Singletons SK0234-003 (64340) M MPX X 142,561,000  142,682,000  121,000 loss CNVs that are Singletons SK0320-003 (79449) M MPX X 143,059,574  143,399,300  339,727 gain CNVs that are Singletons SK0123-004 (60536L) M MPX X 147,974,000  148,479,449  505,449 gain CNVs that are Singletons SK0278-003 (74431) M SPX 1 188,543,244  188,935,335  392,092 gain CNVs that overlap the ACRD MM0149-003 (42382) M MPX 1 191,030,551  191,223,110  192,560 gain CNVs that overlap the ACRD SK0229-003 (62211) M SPX 1 242,451,000  243,113,489  662,489 gain CNVs that overlap the ACRD NA0016-000 (51524L) F SPX 1 243,172,012  243,301,056  129,044 gain CNVs that overlap the ACRD MM0063-003 (46687) F MPX 2 50,780,202 50,859,200  78,999 loss CNVs that overlap the ACRD SK0234-003 (64340) M MPX 2 54,171,783 54,345,700 173,917 gain CNVs that overlap the ACRD SK0188-003 (53664) M SPX 2 112,415,581  112,510,212   94,632 loss CNVs that overlap the ACRD MM0019-003 (42052) M MPX 2 201,286,000  201,317,066   31,067 loss CNVs that overlap the ACRD MM0296-003 (47829) M MPX 2 221,429,610  221,551,000  121,391 loss CNVs that overlap the ACRD NA0004-000 (47490) M SPX 2 235,797,267  236,239,000  441,734 gain CNVs that overlap the ACRD MM0068-003 (60836) M MPX 3  1,720,948  1,795,234  74,287 gain CNVs that overlap the ACRD NA0067-000 (65344L) M SPX 3 61,075,295 61,581,100 505,806 gain CNVs that overlap the ACRD MM0296-003 (47829) M MPX 4   328,851   542,862 214,012 gain CNVs that overlap the ACRD MM0228-004 (47602) M MPX 4 11,820,924 11,983,053 162,130 loss CNVs that overlap the ACRD NA0129-000 (77405) M SPX 4 38,109,899 38,349,444 239,546 gain CNVs that overlap the ACRD SK0188-003 (53664) M SPX 4 61,408,094 61,758,800 350,707 loss CNVs that overlap the ACRD SK0057-003 (40919) M SPX 4 74,105,700 74,464,300 358,600 gain CNVs that overlap the ACRD MM0176-003 (62118L) M MPX 4 91,220,121 91,309,602  89,482 loss CNVs that overlap the ACRD SK0012-003 (58468L) M SPX 4 162,387,402  163,362,655  975,254 gain CNVs that overlap the ACRD SK0012-003 (58468L) M SPX 4 173,324,616  174,954,056  1,629,441  gain CNVs that overlap the ACRD SK0166-003 (36773) M SPX 4 186,788,000  187,118,000  330,001 gain CNVs that overlap the ACRD SK0074-003 (60910L) M MPX 4 188,230,567  190,154,000  1,923,434  gain CNVs that overlap the ACRD SK0083-003 (50800L) M CHR 4 188,232,000  188,253,314   21,315 gain CNVs that overlap the ACRD MM0019-003 (42052) M MPX 4 190,172,765  191,306,043  1,133,279  gain CNVs that overlap the ACRD SK0188-003 (53664) M SPX 5 13,832,700 14,237,600 404,901 gain CNVs that overlap the ACRD NA0078-000 (63727) M MPX 5 79,336,190 79,613,516 277,327 loss CNVs that overlap the ACRD NA0145-000 (82058L) M SPX 5 89,445,869 90,172,900 727,032 gain CNVs that overlap the ACRD SK0167-003 (60966L) F MPX 5 120,343,925  120,474,000  130,076 gain CNVs that overlap the ACRD NA0019-000 (64122L) M SPX 5 120,964,000  121,095,213  131,214 gain CNVs that overlap the ACRD MM0215-004 (47095) M MPX 5 132,619,430  132,732,003  112,574 loss CNVs that overlap the ACRD SK0073-003 (57283L) F CHR 5 134,426,000  134,519,000   93,000 gain CNVs that overlap the ACRD SK0272-003 (70721) F SPX 6 77,622,920 77,673,932  51,012 loss CNVs that overlap the ACRD MM0225-004 (60826) M MPX 6 93,087,482 98,011,900 4,924,419  gain CNVs that overlap the ACRD SK0077-003 (48226) M SPX 6 95,461,800 95,581,304 119,504 loss CNVs that overlap the ACRD SK0087-003 (40450) M MPX 6 97,566,274 97,658,527  92,253 loss CNVs that overlap the ACRD SK0216-003 (58875) M SPX 6 153,519,631  153,791,029  271,398 gain CNVs that overlap the ACRD NA0061-000 (60383) M SPX 7 108,357,049  108,597,525  240,477 loss CNVs that overlap the ACRD SK0226-005 (61360) M SPX 7 118,462,717  118,679,189  216,473 loss CNVs that overlap the ACRD MM0218-004 (45553) M MPX 8 89,598,961 89,678,800  79,840 loss CNVs that overlap the ACRD SK0210-004 (57601) M MPX 9 28,577,800 29,218,800 641,000 loss CNVs that overlap the ACRD SK0273-003 (71182) M MPX 9 70,739,231 70,870,084 130,854 loss CNVs that overlap the ACRD SK0118-003 (52027) M SPX 9 111,652,000  112,212,452  560,453 gain CNVs that overlap the ACRD NA0066-000 (64119L) M SPX 9 116,528,784  116,612,329   83,546 loss CNVs that overlap the ACRD SK0102-004 (31899) M SPX 10  42,611,900 43,266,300 654,400 gain CNVs that overlap the ACRD SK0102-004 (31899) M SPX 10  44,988,900 45,468,800 479,900 gain CNVs that overlap the ACRD NA0109-000 (72873) M SPX 10  112,267,330  112,405,408  138,079 gain CNVs that overlap the ACRD SK0131-003 (39989) F CHR 10  128,501,014  128,592,091   91,078 gain CNVs that overlap the ACRD NA0138-000 (81816L) M SPX 10  133,285,000  133,604,999  320,000 gain CNVs that overlap the ACRD NA0113-000 (82366L) M SPX 11   9,984,119 10,667,800 683,682 loss CNVs that overlap the ACRD SK0218-003 (60340) F CHR 12   1,760,084  1,852,412  92,328 loss CNVs that overlap the ACRD NA0122-000 (76018L) F SPX 13  32,965,700 33,137,655 171,956 gain CNVs that overlap the ACRD NA0117-000 (73621) M SPX 13  42,511,458 42,599,200  87,743 gain CNVs that overlap the ACRD MM0154-003 (56678L) F MPX 13  54,651,953 55,025,229 373,277 gain CNVs that overlap the ACRD SK0328-003 (82302) M SPX 13  103,896,769  103,930,492   33,724 loss CNVs that overlap the ACRD MM0295-003 (46488) M MPX 13  113,361,712  113,646,000  284,289 gain CNVs that overlap the ACRD SK0305-004 (78621) F SPX 14  42,022,286 42,210,026 187,741 loss CNVs that overlap the ACRD SK0320-003 (79449) M MPX 14  45,537,581 45,653,418 115,838 loss CNVs that overlap the ACRD MM0225-004 (60826) M MPX 14  83,373,278 83,435,200  61,923 gain CNVs that overlap the ACRD MM0154-003 (56678L) F MPX 14  106,223,861  106,356,482  132,622 gain CNVs that overlap the ACRD NA0064-000 (63582L) M SPX 15  82,573,421 83,631,697 1,058,276  loss CNVs that overlap the ACRD MM0256-004 (46991) M MPX 15  87,922,400 87,993,909  71,510 gain CNVs that overlap the ACRD SK0266-003 (68257) M SPX 16   6,813,789  6,898,849  85,060 loss CNVs that overlap the ACRD NA0063-000 (60351) M SPX 16  73,397,667 73,657,067 259,400 loss CNVs that overlap the ACRD NA0095-000 (75414L) M SPX 16  74,576,356 74,613,000  36,645 loss CNVs that overlap the ACRD SK0284-003 (72687) F SPX 17  28,985,300 29,960,700 975,400 gain CNVs that overlap the ACRD SK0012-003 (58468L) M SPX 18  27,565,032 27,781,900 216,869 gain CNVs that overlap the ACRD SK0152-003 (41548L) M CHR 18  32,174,061 32,990,975 816,914 loss CNVs that overlap the ACRD SK0147-003 (47544L) F SPX 18  37,509,556 37,950,450 440,895 gain CNVs that overlap the ACRD SK0304-003 (78063) M SPX 18  46,101,841 46,218,000 116,160 gain CNVs that overlap the ACRD NA0138-000 (81816L) M SPX 18  69,282,461 69,330,584  48,124 loss CNVs that overlap the ACRD SK0023-003 (58096) M SPX 21  46,497,675 46,678,820 181,145 gain CNVs that overlap the ACRD NA0112-000 (72340) M SPX X 38,250,331 38,371,333 121,003 gain CNVs that overlap the ACRD SK0283-003 (72309) F CHR 4 44,762,996 44,858,504  95,508 gain CNVs that overlap the ACRD MM0010-005 (47372) M MPX 4 44,773,367 44,846,800  73,434 gain CNVs that overlap the ACRD NA0093-000 (66999) M SPX 4 44,773,367 44,846,800  73,433 gain CNVs that overlap the ACRD MM0109-003 (46486) F SPX 4 189,538,747  189,825,000  286,254 gain CNVs that overlap the ACRD SK0112-003 (46100) M MPX 4 189,580,553  190,228,000  647,447 gain CNVs that overlap the ACRD

Wide-ranging prevalence frequencies of cytogenetically detectable chromosomal abnormalities in ASD, and the inability of microarray scans to find balanced abnormalities, prompted karyotyping to be performed. Karyotyping (and FISH) also provided the ability to characterize the chromosomal context (e.g. ring chromosomes) of some of the CNV regions, something not possible using microarrays alone. Therefore, 313 unbiased idiopathic cases where blood was available were examined and 5.8% (18/313) cases were found to have balanced (11) or unbalanced (7) karyotypes (all unbalanced karyotypic changes (7) were also found by microarray analysis and are included in the CNV statistics). The genomic characteristics of all CNVs are shown in the Autism Chromosome Rearrangement Database (see FIG. 3). In this study, CNV loss and gain will typically equate to a standard deletion or duplication. In some cases a duplication of only part of a gene could lead to its disruption (Table 5), and there are also positional effects on gene expression to consider.

De Novo, Overlapping/Recurrent, and Inherited Structural Variants

Structural variants found in ASD cases were initially prioritized to possibly be etiologic if they were not in controls and, (i) de novo in origin (25 cases) (see Table 5 below), (ii) overlapping (27 cases at 13 loci) in two or more unrelated samples (see Table 7 below), (iii) recurrent (same breakpoints) in two or more unrelated samples (four cases at two loci), (iv) or inherited the remainder). In a proof of principle analysis, CNVs were found at known ASD loci: NLGN4 and 22q, 15q, SHANK3 and NRXN1 in categories i, ii, iii, and iv, respectively. ASD structural variants found in controls (eg. NRX1) could also be involved.

TABLE 5 De Novo Rearrangements in ASD cases FamID (DNA)¹ Sex Type Chromosome² Size (bp)³ CNV Genes⁴ Phenotype Comments⁵ 1 SK0181-004 (52191) M CHR (SPX) 3p14.1-3p13 (a) 5,346,900 loss 13 genes IQ = 107 t(6; 14)(q13; q21)(k) N/A none 11 genes Dysmorphology 2 SK0152-003 (41548) M CHR (MPX)⁶ 3p25.1-p24.3 (a) 1,409,600 loss 12 genes IQ = unknown 5p15.31-p15.2 (a) 3,429,389 loss 8 genes 12q12 (a) 422,842 loss 4 genes t(5; 7)(p15p13) (k) N/A none CDH18 3 SK0215-006 (58449) M CHR (SPX) 1p21.3 (a) 1,092,500 loss DPYD whole IQ = 38, SLI 4 SK0205-004 (56242) F CHR (SPX) 5p15.33-5p15.2 (k) 13,800,984 loss 46 genes IQ = unknown, Cri du chat 5 SK0083-003 (50800) M CHR (SPX) 7q31.1-q31.31 (k) 11,023,507 loss 25 genes IQ = 76 6 SK0131-003 (39989) F CHR (SPX) 7q31.1-q32.2 (k) 15,486,722 loss >50 genes IQ = 95, SLI 7 SK0243-003 (67941) M CHR (SPX) 15q23-q24.2 (k) 4,289,500 loss >50 genes IQ = unknown, SLI 8 SK0073-003 (57283) F CHR (SPX) 15q11.2-q13.3 (k) 11,922,600 gain >50 genes IQ = unknown 9 SK0245-005 (68517) M CHR (SPX) 15q11.2-q13.3 (k) 11,871,747 gain >50 genes IQ = unknown 10 SK0218-003 (60340) F CHR (MPX)⁴ 18q21.32-18q23 (k) 20,358,999 loss >50 genes IQ = unknown, seizures, dysmorphology 11 NA0039-000 (69736) F CHR (SPX) 22q13.31-q13.33 (k) 3,231,700 loss 41 genes IQ = unknown 12 NA0097-000 (82361) F CHR (SPX) Xp22.33-p22.31 (a) 5,825,311 loss 21 genes + NLGN4 IQ = unknown 13 SK0283-003 (72309) F CHR (SPX) 47, XX, ring chr1 (k) N/A gain >50 genes IQ = 38 14 SK0133-003 (46012 M CHR (SPX) t(5; 8; 17)(q31.1; N/A none 5 genes IQ = unknown q24.1; q21.3) (k) 15 NA0002-000 (52026) M SPX 7q36.2 (a) 66,462 loss DPP6 exonic IQ = unknown 16 SK0262-003 (68609) M SPX 8p23.3 (a) 791,089 gain DLGAP2 exonic IQ = unknown 17 MM0278-003 (57788) M SPX 12q24.21-q24.33 (a) 18,218,000 gain >50 genes IQ = 36 18 NA0067-000 (65344) M SPX 16q24.3 (a) 265,667 loss ANKRD11 exonic IQ = unknown 19 MM0088-003 (45562) F MPX 16p11.2 (a) 675,829 loss 28 genes IQ = 87 20 SK0102-004 (31899) M SPX 16p11.2 (a) 432,600 gain 24 genes IQ = 74, Epilepsy 21 SK0244-003 (69183) M SPX 21q22.3 (a) 353,936 gain 4 genes IQ = 80 22 MM0109-003 (46486) F SPX 20q13.33 (a) 1,427,661 gain 44 genes IQ = unknown 22q13.33 (a) 276,702 loss 13 genes + SHANK3 23 SK0119-003 (35190) M MPX⁴ 22q11.21 (a) 2,771,300 loss >50 genes IQ = 58, VCF syndrome 24 SK0297-003 (76066) M SPX-MZ 22q11.21 (a) 4,281,262 gain >50 genes IQ = 107, dysmorphology 25 SK0306-004 (78681) F SPX Xp11.23-11.22 (a) 4,643,367 gain >50 genes IQ = 87 ¹Table is sorted based on family type. Probands with abnormal karyotypes (CHR) (1-14) are separated from probands belonging to simplex (SPX) and multiplex (MPX) families with normal karyotypes (15-25). ²De novo event detected by either karyotype (k) or microarray (a) ³De novo CNV/translocation has been confirmed by at least one of karyotype, FISH, or qPCR. CNV size is based on array results. The breakpoints have not been accurately defined, and CNVs may be smaller or larger than posted. ⁴When only a single gene is involved if the CNV intersects (suggesting it may disrupt the gene) the term ‘exonic’ is used and if the CNV encompasses the entire gene the term ‘whole’ is used. ⁵For multiplex families the de novo events were not detected in affected siblings. **comment on case 25 that is also in Table 3(see entry #2

TABLE 6 Recurrent and overlapping loci in ASD Chromosome FamID (DNA) Sex Type¹ Size (bp)² CNV Origin Genes³ Phenotype Comments 1 2q14.1 SK0147-003 (47544) F SPX 478,370 loss Paternal DPP10 exonic IQ = unknown, NF1 SK0288-003 (75420) F SPX-MZ 105,120 gain Paternal DPP10 intronic IQ = 83 2 2q32.1 SK0306-004 (78681) F SPX  97,130 loss Unknown None IQ = 87 NA0030-000 (55240) M SPX 112,323 loss Unknown None IQ = unknown 3 6q22.31 MM0220-003 (61180) M MPX 318,000 gain Paternal PLN, c6orf204 IQ = unknown whole NA0025-000 (60490) M SPX 293,989 gain Paternal PLN, c6orf204 IQ = unknown whole 4 7q36.2 SK0190-003 (54742) M SPX 1,780,000  gain Maternal DPP6 whole IQ = 82 SK0115-003 (40555) M SPX 274,000 gain Unknown DPP6 exonic IQ = unknown SK0058-003 (59963) M MPX  16,788 gain Maternal DPP6 intronic IQ = 111 NA0002-000 (52026) M SPX  66,462 loss De novo DPP6 exonic IQ = unknown 5 8q11.23 SK0143-003 (36812) M SPX 285,200 gain Unknown UNQ9433 whole, IQ = 66 RB1CC1 exonic Apraxia, CHD, Seizures MM0236-004 (46475) M MPX 271,679 gain Unknown RS1CC1 exonic IQ = 99 6 9p24.1 SK0270-003 (71341) M SPX  38,900 loss Unknown none IQ = 91, SLI MM0103-003 (42387) M MPX  34,950 loss Paternal none IQ = 107 7 11p12 MM0272-003 (45563) M MPX 262,938 loss Maternal none IQ = 111, Seizures SK0167-003 (60966) F MPX 192,846 loss Unknown none IQ = 91 8 13q21.32 SK0023-003 (58096) M SPX 189,438 gain Unknown PCDH9 intronic IQ = 91, Seizures MM0299-003 (51674) F MPX 172,401 gain Paternal PCDH9 intronic IQ = 39 9 15q11.2-q13.3 SK0073-003 (57283) F CHR 11,922,600   gain De novo >50 genes IQ = unknown SK0245-005 (68517) M CHR 11,871,747   gain De novo >50 genes IQ = unknown 10 16p12.1 MM0109-003 (46486) F SPX 1,246,288  gain Maternal 8 genes IQ = unknown MM0289-003 (42267) F MPX 802,555 loss Maternal 5 genes IQ = 63 11 16p11.1 NA0133-000 (78119) F SPX 525,319 gain Maternal 29 genes IQ = unknown SK0102-004 (31899) M SPX  432,600⁴ gain De novo 24 genes IQ = 64, Epilepsy MM0088-003 (45562) F MPX 675,829 loss De novo 32 genes IQ = 87 12 22q11.2 SK0119-003 (35190) M MPX 2,771,300  loss De novo >50 genes IQ = 58, VCF syndrome SK0091-004 (46407) F MPX 4,281,262  gain Paternal >50 genes IQ = 126 SK0297-003 (76066) M SPX-MZ 4,281,262  gain De novo >50 genes IQ = 107, dysmorphology SK0323-003 (80022) M MPX 743,100 gain Unknown 7 genes IQ = unknown 13 22q13.31 SK0123-004 (60536) M MPX 601,528 gain Maternal none IQ = 93 MM0102-003 (47598) M MPX  80,380 loss Maternal none IQ = 70 ¹Families are grouped based on simplex (SPX), multiplex (MPX) and chromosomal abnormalities (CHR). Simplex families with affected monozygotic twins is denoted as SPX-MZ. The de novo cases also appear in Table 2 and some of the family pedigrees are shown in FIG. 2 and Supplemental FIG. 2. ²CNV size is based on array results. The breakpoints have not been accurately defined, and CNVs may be smaller or larger than posted. ³When only a single gene is involved if the CNV intersects (suggesting it may disrupt the gene) the term ‘exonic’ is used and if the CNV encompasses the entire gene the term ‘whole’ is used. ⁴CNV is only called by one algorithm

By testing parental DNA and validating CNVs, a de novo mutation rate of 7.1% (4/56) and 2.0% (1/49) was observed in idiopathic simplex and multiplex families, respectively. There was parental information for 13 of 18 cases discovered to carry cytogenetic abnormalities and 7 (6 simplex, 1 multiplex) of these were de novo in origin. Since only 1/7 (from a simplex family) of these was balanced and directly interrupting a gene, it was estimated that this class of rearrangements had much less of a contribution than CNVs to the total rate of de novo and structural variation in the present cohort.

The collective data identified 25 de novo cases (Table 5) and in three, two or more events were identified. Notably, in family SK0152 (FIG. 4 a) there were four de novo events. In MM019 (FIG. 4 b) there were two de novo deletions, one leading to haplo-insufficiency of SHANK3.

The 13 loci where overlapping ASD-specific CNVs were found are likely indicative of ASD-susceptibility since they arise in two or more unrelated families. In six, gains and losses often encompassing entire genes were observed at the same locus (Table 6) suggesting general gene dysregulation to be involved.

Using q-PCR or by assessing SNP patterns, 196 inherited CNVs (90 maternal and 106 paternal) were confirmed. No sub-grouping of these demonstrated obvious parent-of-origin effects (the two chromosome 15q11-q13 duplications detected were both de novo in origin). A 160 kb deletion was detected in a male inherited from a carrier mother, leading to a null PTCHD1 in the proband and his dizygotic twin brother (FIG. 4 c). There were also instances where apparently balanced inherited translocations were accompanied by de novo deletions in the offspring (eg. DPYD) (FIG. 4 d).

Candidate ASD-Susceptibility Genes and Loci Identified

New ASD candidates identified were those with a structural change (either de novo or found in two or more unrelated ASD cases, or for the X chromosome an allele being transmitted maternally from an unaffected carrier) specific to that gene, including ANKRD11, DLGAP2, DPP6, DPP10, DPYD, PCDH9 and PTCHD1 (Tables 5 and 6). As previously noted, NLGN4, SHANK3 and NRXN1 were also identified. The PCDH9 and NRXN1 genes are also found as CNVs in controls in the DGV (Database of Genomic Variants).

Additional positional candidate genes identified were those found interrupted by balanced cytogenetic breakpoints including NEGR1, PIP5K1B, GABRG1, KLHL3, STK3, ST7, SATB2 (Table 1). Moreover, 77 CNVs in the stringent dataset overlapped with the Autism Chromosome Rearrangement Database providing a second line of evidence for involvement (FIG. 2). For example, a 4.6 Mb de novo duplication at Xp11.23-11.22 was detected in a female SK0306-004 (Table 5) and a male in the database.

DPP6 and DPP10 emerge as being positional and functional candidates. DPP6 (˜1.5 Mb in size at 204.1) and DPP10 (˜1.3 Mb at 7q36.2) code for accessory trans-membrane dipeptidyl peptidase-like subunits that affect the expression and gating of Kv4.2 channels (KCND2). Kv4.2 channels function in regulation of neurotransmitter release and neuronal excitability in the glutamatergie synapse at the same sites where SHANK3 and the NLGN gene products are found. In addition, autism balanced breakpoints have been mapped near KCND2 at 7q31.

For DPP10 there are inherited CNV gains and losses (Table 5, FIG. 4). De novo and inherited CNVs were found at the multi-transcript DPP6 gene. A 66 kb de novo loss encompassing exons 2 and 3 is found in a male in family NA0002 (FIG. 4 e). In family SK0190, the male proband and an unaffected female sibling both carry a CNV gain inherited from an unaffected mother (FIG. 4 f) that encompassed the entire DPP6. A 270 kb gain was found in SK0115-003 that extends across the first exon (which may disrupt the functional gene) and SK0058-003 carries a maternally-inherited 16 kb intronic CNV gain (Table 1; FIG. 5).

Medical Genetics

Structural variants overlapping loci involved in medical genetic conditions including Waardenburg Type IIA (3p14.1), speech and language disorder (7q31), mental retardation (MR)(15q23-q24, 16p11.2) and velocardialfacial syndrome (VCFS) (22q13) were identified (Table 5), amongst others. Identification of the structural variant at these loci led to clinical re-assessment and either identification or refinement of the diagnosis, for additional syndromic features. Other instances (eg. SK0186-PTCHD1 deletion) (FIG. 4 c) prompted re-testing of the entire family and eventually a diagnosis of mild-ASD in a previously undiagnosed sibling. This family was then redesignated multiplex as opposed to simplex.

The identification of a de novo deletion (2.7 Mb) at 22q11.2 in two ASD brothers led to their re-examination and diagnosis for VCFS. The re-testing also further defined the siblings to be at opposite ends of the ASD spectrum (FIG. 6). Larger duplications (4.3 Mb) of this same region in two other ASD families (SK0289 and SK0091) did not cause VCFS (Table 6); however, in SK0091 the variant was inherited from a normal father and not found in an affected male sibling.

A recurrent ˜500 kb duplication at 16p11.2 in two ASD families (SK0102 and NA0133) (FIGS. 4 and 5) was also discovered. As with DPP6/DPP10 and 22q11.2, there were carriers of these structural variants without ASD. In a third family (MM0088), the proband has a larger 676 kb de novo deletion and it is only detected in one of two ASD siblings. (FIG. 4 g).

In sum, using the genome-wide scanning approach, numerous new putative-ASD loci (Tables 4 and 5, FIG. 2) were identified. Generally, ASD loci include (i) those that contain genes functioning in the PSD, (ii) and/or chromosomal regions previously shown to be involved in mental retardation, and (iii) involve dysregulation of gene expression.

CNVs that implicate ASD loci include the SHANK3, NLGN, and NRXN1-PSD genes and also identify novel loci at DPP6 and DPP10 (amongst others including PCDH9, RPS6KA2, RET from the full dataset) were identified.

Lastly, six unrelated ASD cases were identified (Table 6) that had either CNV gains or losses at the same locus which indicate that gene expression of genes in these regions are related to the development of speech and language and/or social communication in humans, as in SHANK3 and genes in the Williams-Beuren syndrome locus.

Example 2 PTCHD1 as a Marker of ASD

As set out above, a genome scan with Affymetrix 500K SNP Arrays was used to identify a CNV deletion on chromosome Xp22.11 that spans exon 1 of the PTCHD1 gene. Exon 1 is shown bolded in FIG. 7 spanning nucleotide positions 1-359. The Cdna sequence of the PTCHD1 gene (NM_(—)173495) as well as the amino acid sequence of the corresponding encoded protein is illustrated in FIG. 7 which illustrates a genomic size of: 59325, an exon/coding exon count of 3 encoding a protein of 783 amino acids.

The deletion was determined to be an ˜156 kb deletion on Xp22.11 on a male proband. The physical position of this CNV is chrX:22, 962,800-23, 119,000 (UCSC 2004 Assembly). The deletion is flanked by SNP probes rs7055928 and rs1918560 (at 22.956 and 23.133 Mb from the Xp terminus, respectively). The most proximal and distal SNPs (from the Affymetrix SNP microarrays) within the deleted region, as determined by the SNP microarray analysis, are rs7879064 (23.119 Mb) and rs4828958 (22.972 Mb). PCR amplicons from within the deleted region were used to confirm the deletion by Qpcr (PCR primers and locations are given below). This deletion spans the entire exon 1 of the PTCHD1 gene (NM_(—)173495). Analysis of both Sty and Nsp chips data identified this event and was further validated using PCR and QPCR techniques. The following primers were used:

(SEQ ID NO: 1) PTCHD-CNV1F ATTCGCAGTTCCTTCGTCTT (SEQ ID NO: 2) PTCHD-CNV1R AAAGTGGATTGATCGGTTCC (SEQ ID NO: 3) PTCHD-CNV2F GCTTGAGGACGTGTTTCTCC (SEQ ID NO: 4) PTCHD-CNV2R CTAGGAGAGGTGGCGCTCT

This CNV is autism specific as it was not present in the Database of Genomic Variants (DGV) and in other controls. Furthermore, the segregation of this deletion was characterized in family and it was identified that the deletion was transmitted from a heterozygous mother. A male sibling also had language deficits.

Mutation screening of PTCHD1 in N=400 autism patients was conducted in the usual manner. The following primers were used:

(SEQ ID NO: 5) PTCHD1-x1F AGCGTGCGCCTCGCCCT (SEQ ID NO: 6) PTCHD1-x1R TCCTTGTCCAGGAGGCTGGGA (SEQ ID NO: 7) PTCHD1-x1Bf GCGCCCGCTCTGCTCTA (SEQ ID NO: 8) PTCHD1-x1Br TCCTTGTCCAGGAGGCTGGGA (SEQ ID NO: 9) PTCHD1-x2-F GAATGTCCACCCTCTCCAAA (SEQ ID NO: 10) PTCHD1-x2-R AAGGCTACTCCTGGCCTTTT (SEQ ID NO: 11) PTCHD1-x3a-F CTTTGACCCAGTAGTCCCTCA (SEQ ID NO: 12) PTCHD1-x3a-R GCACAAACCCCTTGGTGTA (SEQ ID NO: 13) PTCHD1-x3b-F TGTGATTGGGTTTTACATATATGAGTC (SEQ ID NO: 14) PTCHD1-x3b-R AGGTCAGATTTGAAGGCACAG (SEQ ID NO: 15) PTCHD1-x3c-F AAAAATGCCCTGGAAGTGC (SEQ ID NO: 16) PTCHD1-x3c-R TGTGTGAATTCTCATAACAACTCCT

The mutation screening revealed an I173V mutation.

Example 3 Identification of Additional Markers of ASD

By sequencing the entire coding region of PTCHD1 in 900 unrelated ASD cases, six missense mutations were identified in six unrelated ASD probands (Table 7, FIG. 8). For clinical details see Table 8.

TABLE 7 XCI No. of Status of Control Sex of Family Carrier Population Frequency Chromosomes Subject ID Exon Mutation Nucleotide Proband Transmission Type Mother Ancestry in ASD Tested Family 1 1 167-kb deletion, M Mother Multiplex Skewed European 1 in 427 2067 disrupts PTCHD1 (M = 769 gene at Xp22.11 F = 1298) Family 1 1 167-kb deletion, M Mother Multiplex Skewed European 1 in 427 2067 disrupts PTCHD1 (M = 769 gene at Xp22.11 F = 1298) Family 2 2 I173V 517A > G M Mother Multiplex Random European\Mixed 2 in 900 659 (M = 219 F = 220) Family 3 2 I173V 517A > G M Mother Simplex Random European 2 in 900 659 (M = 219 F = 220) Family 4 2 V195I 583G > A M Mother Simplex NC European 1 in 900 659 (M = 219 F = 220) Family 5 2 ML336-7II 1008- M Mother Simplex Random Asian 1 in 900 751* 9GC > TA (M = 249 F = 251) Family 6 3 E479G 1436A > G M Mother Multiplex Random European 1 in 900 427 (M = 137 F = 145) Family 7 1 L73F 217C > T M Mother Multiplex NC Not Available 1 in 900 427 (M = 137 F = 145) *Out of 751 control chromosomes tested, N = 92 were Asian

TABLE 8 Subject ID Sex Mutations Clinical Details Family History Comments Family 1 M 167-kb del Meet ADI and ADOS-1 criteria for diagnosis of autism. Difficulty Maternal history of Severe colic with conversations, echoed words, repetitive interests, delay in social learning problem and during early use of language. Attention Deficit and Hyperactivity Disorder articulation difficulties. childhood (ADHD). No mental retardation (MR). Paternal history of ADHD Non-Verbal IQ = 42% ile like features. Family 1 M 167-kb del Meet ADI and ADOS-1 criteria for diagnosis of autism. Difficulty Maternal history of Severe colic with conversations, echoed words, repetitive interests, delay in social learning problem and during early use of language. Attention Deficit and Hyperactivity Disorder articulation difficulties. childhood (ADHD). No mental retardation (MR). Paternal history of ADHD Non-Verbal IQ = 23% ile like features. Family 2 M I173V Meet ADI and ADOS-1 criteria for diagnosis of autism. Highly Father had type II diabetes repetitive language and behaviour, motor mannerisms, extremely hyperactive, poor motor coordination and mental retardation, Lang: receptive = 40, <1% ile, expressive = 40, <1% ile Family 3 M I173V Meet ADI and ADOS-1 criteria for diagnosis of autism. Meet ADI No family history of PDD and ADOS-1 criteria for diagnosis of autism. ADI social score = 25, ADI communication score = 21, ADI Restricted, Repetitive, and Stereotyped Behavior Score = 11, ADI development score = 3, Normal IQ, M V195I Diagnosed with autism at the age of 3 years and 4 months. Meet ADI No family history of PDD FRX and head and ADOS-1 criteria for diagnosis of autism. Severe expressive and CT scan was receptive language delay. No dysmorphology observed. normal Family 5 M ML336-7II Meet ADI and ADOS-1 criteria for diagnosis of autism. ADI social Father died of leukemia Minor score = 26, ADI communication score = 14, ADI stereotype score = 5 thalassemia ADI development score: 4, ADOS social + communication score = 20, ADOS Restricted, Repetitive, and Stereotyped Behavior Score = 3, Some traits were observed that could be related to schizophrenia. Family 6 M E479G Diagnosed with high functioning autism. No family history of PDD Family 7 M L73F Meet ADI and ADOS-1 criteria for diagnosis of autism

All these mutations resulted in the substitution of highly conserved amino acids, and were inherited from unaffected carrier mothers. Based on in silico protein modeling, three mutations (L73F, I173V, V195I) are present in a predicted amino acid loop that sits outside of the cell membrane. This loop is posited to interact with the ligand, Hh. Another mutation, the 2-amino acid substitution ML336-337II was present within a predicted transmembrane domain. Finally, the E479G mutation was present within a predicted cytoplasmic amino acid loop. In five out of six families, these mutations segregated with the phenotype. Controls (439) were tested for the I173V and V195I mutations, 500 controls for ML336-337II, and 282 controls for L73F and E479G. None of these mutations were present in controls. Furthermore, the fact that these mutations were all maternally inherited to male probands, and were not observed in our control populations, indicates that the mutations are associated with ASD. In turn, it is reasonable to assume that these mutations contribute to the etiology of autism, and perhaps in-combination with other disease-related loci, give rise to the ASD phenotype.

Interestingly, in two of the ASD families reported in Tables 7/8 (Family-2 & Family-4), other ASD-related CNVs were identified. In family 2, in addition to I173V mutation, a de novo ˜1.0 Mb loss at 1p21.3 resulting in deletion of the entire DPYD gene (NM_(—)000110.3) was identified. DPYD encodes a rate-limiting enzyme, dihydropyrimidine dehydrogenase (DPD), involved in pyrimidine metabolism. Complete DPD deficiency results in highly variable clinical outcomes, with convulsive disorders, motor retardation, and mental retardation being the most frequent manifestations. In Family-4, in addition to the V195I mutation, a 66 Kb de novo loss at 7q36.2 was identified resulting in deletion of DPP6 exon 3, and 33 amino acids towards the N-terminal end of the DPP6 protein. These cases evidence digenic involvement in ASD.

The ability of these PTCHD1-mutants to repress Gli2 expression was compared with wild type to determine if there was loss of function in the mutants. NIH10T1/2 fibroblasts were transfected with CMV-empty vector, a Gli-responsive promoter fused to the Luciferase gene (Gli2 pro), β-Gal (normalization) and PTCHD1 mutant expression plasmids. A mild loss of function of at least the E479G and ML336-711 mutants resulted in increased expression of Gli2 compared to wild type. 

We claim:
 1. A method of determining the risk of ASD in an individual comprising: probing a nucleic acid-containing sample obtained from the individual for a genomic sequence mutation in at least one gene selected from the group consisting of PTCHD1, SHANK3, NFIA, DPP6, DYPD, DPP10, GPR98, PQBP1, ZNF41 and FTSJ1, wherein identification of a mutation that modulates the expression of at least one of said genes is indicative of a risk of ASD.
 2. A method as defined in claim 1, wherein the genomic sequence variation is in the PTCHD1 gene.
 3. A method as defined in claim 1, wherein the genomic sequence mutation is a deletion of at least a portion of exon 1 of PTCHD1.
 4. A method as defined in claim 1, wherein the genomic sequence mutation is an intronic gain in DPP10.
 5. A method as defined in claim 1, wherein the genomic sequence mutation is an exonic loss in DPP10.
 6. A method as defined in claim 1, wherein the genomic sequence mutation is an exonic loss encompassing at least a portion of exons 2 and 3 in DPP6.
 7. A method as defined in claim 1, wherein the genomic sequence mutation is a gain in DPP6 selected from at least one of the group consisting of the entire DPP6 gene, a 270 kb exonic gain in exon 1 and a 16 kb intronic gain.
 8. A method as defined in claim 1, wherein the genomic sequence mutation is a loss in the SHANK3 gene.
 9. A method as defined in claim 1, wherein the genomic sequence mutation is a loss of the DYPD gene.
 10. A method as defined in claim 1, wherein the genomic sequence mutation is at least one missense mutation in PTCHD1 resulting in at least one amino acid substitution in the encoded protein selected from the group consisting of L73F, I173V, V195I, ML336-337II and E479G.
 11. A method as defined in claim 1, wherein the genomic sequence mutation is selected from the group consisting of a deletion of at least a portion of exon 1 of PTCHD1; an intronic gain in DPP10; an exonic loss in DPP10; an exonic loss encompassing at least a portion of exons 2 and 3 in DPP6; a gain in DPP6 selected from at least one of the group consisting of the entire DPP6 gene, a 270 kb exonic gain in exon 1 and a 16 kb intronic gain; a loss in the SHANK3 gene; a loss of the DYPD gene; and at least one missense mutation in PTCHD1 resulting in at least one amino acid substitution in the encoded protein selected from the group consisting of L73F, I173V, V195I, ML336-337II and E479G.
 12. A method of determining the risk of ASD in an individual comprising: screening a biological sample from the individual for abnormal levels of at least one gene product expressed by a gene selected from the group consisting of PTCHD1, SHANK3, NFIA, DPP6, DPP10, DYPD, GPR98, PQBP1, ZNF41 and FTSJ1, wherein a determination that at least one of said gene products is expressed at a level that varies from the expression level in a healthy non-ASD individual is indicative of a risk of ASD.
 13. The method as defined in claim 12, wherein the biological sample is screened for abnormal levels of the PTCHD1 gene product.
 14. A method of determining the risk of ASD in an individual comprising: screening a nucleic acid-containing sample from the individual for at least one genomic sequence variation that modulates the expression of PTCHD1, wherein identification of at least one of said genomic sequence variations is indicative of a risk of ASD in the individual.
 15. A method as defined in claim 14, wherein the genomic sequence variation is in the PTCHD1 gene.
 16. A method as defined in claim 14, wherein the genomic sequence variation is a deletion of at least a portion of exon 1 of PTCHD1.
 17. A method as defined in claim 14, wherein the genomic sequence variation is at least one missense mutation in PTCHD1 resulting in at least one amino acid substitution in the encoded protein selected from the group consisting of L73F, I173V, V195I, ML336-337II and E479G. 